=>> Building biology/diamond build started at Fri Apr 5 15:30:50 BST 2024 port directory: /usr/ports/biology/diamond package name: diamond-2.1.9 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: jrm@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 414 Feb 8 11:33 /usr/ports/biology/diamond/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: 92b051a290 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 10 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 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 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PATH=/ccache/libexec/ccache:/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 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CCACHE_DIR="/root/.ccache" 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=13.2 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--- 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 #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 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 --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-2.1.9 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> diamond-2.1.9 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of diamond-2.1.9 =========================================================================== =================================================== ===== 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-2.1.9 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by diamond-2.1.9 for building => SHA256 Checksum OK for bbuchfink-diamond-v2.1.9_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-2.1.9 for building ===> Extracting for diamond-2.1.9 => SHA256 Checksum OK for bbuchfink-diamond-v2.1.9_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-2.1.9 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> diamond-2.1.9 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.28.3.pkg [pkg-builder.dan.net.uk] Installing cmake-core-3.28.3... [pkg-builder.dan.net.uk] `-- Installing expat-2.6.1... [pkg-builder.dan.net.uk] `-- Extracting expat-2.6.1: .......... done [pkg-builder.dan.net.uk] `-- Installing jsoncpp-1.9.5... [pkg-builder.dan.net.uk] `-- Extracting jsoncpp-1.9.5: .......... done [pkg-builder.dan.net.uk] `-- Installing libuv-1.48.0... [pkg-builder.dan.net.uk] `-- Extracting libuv-1.48.0: .......... done [pkg-builder.dan.net.uk] `-- Installing openssl-3.0.13_1,1... [pkg-builder.dan.net.uk] `-- Extracting openssl-3.0.13_1,1: .......... done [pkg-builder.dan.net.uk] `-- Installing rhash-1.4.4_1... [pkg-builder.dan.net.uk] | `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] | `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] `-- Extracting rhash-1.4.4_1: .......... done [pkg-builder.dan.net.uk] Extracting cmake-core-3.28.3: .......... done ===> diamond-2.1.9 depends on file: /usr/local/bin/cmake - found ===> Returning to build of diamond-2.1.9 ===> diamond-2.1.9 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.11.1,2.pkg [pkg-builder.dan.net.uk] Installing ninja-1.11.1,2... [pkg-builder.dan.net.uk] `-- Installing python39-3.9.18_1... [pkg-builder.dan.net.uk] | `-- Installing libffi-3.4.4_1... [pkg-builder.dan.net.uk] | `-- Extracting libffi-3.4.4_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing mpdecimal-2.5.1... [pkg-builder.dan.net.uk] | `-- Extracting mpdecimal-2.5.1: .......... done [pkg-builder.dan.net.uk] | `-- Installing readline-8.2.10... [pkg-builder.dan.net.uk] | `-- Extracting readline-8.2.10: .......... done [pkg-builder.dan.net.uk] `-- Extracting python39-3.9.18_1: .......... done [pkg-builder.dan.net.uk] Extracting ninja-1.11.1,2: ..... done ===== Message from python39-3.9.18_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===> diamond-2.1.9 depends on executable: ninja - found ===> Returning to build of diamond-2.1.9 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for diamond-2.1.9 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/diamond/work/.build CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 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 Clang 14.0.5 -- The CXX compiler identification is Clang 14.0.5 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /ccache/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: /ccache/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 -- Found ZLIB: /usr/lib/libz.so (found version "1.2.13") -- 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 -- Configuring done (2.8s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_COLOR_MAKEFILE CMAKE_CXX_FLAGS_DEBUG CMAKE_C_FLAGS_DEBUG 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 =========================================================================== =================================================== ===== 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-I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -DEigen=Eigen_AVX2 -MD -MT CMakeFiles/arch_avx2.dir/src/dp/ungapped_simd.cpp.o -MF CMakeFiles/arch_avx2.dir/src/dp/ungapped_simd.cpp.o.d -o CMakeFiles/arch_avx2.dir/src/dp/ungapped_simd.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/dp/ungapped_simd.cpp [ 14% 28/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -DEigen=Eigen_AVX2 -MD -MT CMakeFiles/arch_avx2.dir/src/dp/pfscan/pfscan.cpp.o -MF CMakeFiles/arch_avx2.dir/src/dp/pfscan/pfscan.cpp.o.d -o CMakeFiles/arch_avx2.dir/src/dp/pfscan/pfscan.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/dp/pfscan/pfscan.cpp [ 15% 29/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -DEigen=Eigen_AVX2 -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-2.1.9/src/dp/swipe/anchored_wrapper.cpp [ 15% 30/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -DEigen=Eigen_AVX2 -MD -MT CMakeFiles/arch_avx2.dir/src/dp/score_profile.cpp.o -MF CMakeFiles/arch_avx2.dir/src/dp/score_profile.cpp.o.d -o CMakeFiles/arch_avx2.dir/src/dp/score_profile.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/dp/score_profile.cpp [ 16% 31/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/run/main.cpp.o -MF CMakeFiles/diamond.dir/src/run/main.cpp.o.d -o CMakeFiles/diamond.dir/src/run/main.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/run/main.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/run/main.cpp:31: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/run/../cluster/cluster_registry.h:21: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/run/../cluster/cluster.h:28: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/run/../cluster/../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/run/../cluster/../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 16% 32/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/basic/config.cpp.o -MF CMakeFiles/diamond.dir/src/basic/config.cpp.o.d -o CMakeFiles/diamond.dir/src/basic/config.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/basic/config.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/basic/config.cpp:42: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/basic/../cluster/cluster_registry.h:21: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/basic/../cluster/cluster.h:28: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/basic/../cluster/../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/basic/../cluster/../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 17% 33/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/stats/score_matrix.cpp.o -MF CMakeFiles/diamond.dir/src/stats/score_matrix.cpp.o.d -o CMakeFiles/diamond.dir/src/stats/score_matrix.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/score_matrix.cpp [ 17% 34/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/data/queries.cpp.o -MF CMakeFiles/diamond.dir/src/data/queries.cpp.o.d -o CMakeFiles/diamond.dir/src/data/queries.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/queries.cpp [ 18% 35/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/data/seed_histogram.cpp.o -MF CMakeFiles/diamond.dir/src/data/seed_histogram.cpp.o.d -o CMakeFiles/diamond.dir/src/data/seed_histogram.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/seed_histogram.cpp [ 18% 36/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/output/daa/daa_record.cpp.o -MF CMakeFiles/diamond.dir/src/output/daa/daa_record.cpp.o.d -o CMakeFiles/diamond.dir/src/output/daa/daa_record.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/daa/daa_record.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/daa/daa_record.cpp:21: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/daa/../output.h:34: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/daa/../output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/daa/../output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 19% 37/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/util/command_line_parser.cpp.o -MF CMakeFiles/diamond.dir/src/util/command_line_parser.cpp.o.d -o CMakeFiles/diamond.dir/src/util/command_line_parser.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/util/command_line_parser.cpp [ 19% 38/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/util/seq_file_format.cpp.o -MF CMakeFiles/diamond.dir/src/util/seq_file_format.cpp.o.d -o CMakeFiles/diamond.dir/src/util/seq_file_format.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/util/seq_file_format.cpp [ 20% 39/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/util/util.cpp.o -MF CMakeFiles/diamond.dir/src/util/util.cpp.o.d -o CMakeFiles/diamond.dir/src/util/util.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/util/util.cpp [ 20% 40/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/basic/basic.cpp.o -MF CMakeFiles/diamond.dir/src/basic/basic.cpp.o.d -o CMakeFiles/diamond.dir/src/basic/basic.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/basic/basic.cpp [ 21% 41/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/basic/hssp.cpp.o -MF CMakeFiles/diamond.dir/src/basic/hssp.cpp.o.d -o CMakeFiles/diamond.dir/src/basic/hssp.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/basic/hssp.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/basic/hssp.cpp:24: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/basic/../output/output.h:34: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/basic/../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/basic/../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 21% 42/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/dp/ungapped_align.cpp.o -MF CMakeFiles/diamond.dir/src/dp/ungapped_align.cpp.o.d -o CMakeFiles/diamond.dir/src/dp/ungapped_align.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/dp/ungapped_align.cpp [ 22% 43/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/run/tools.cpp.o -MF CMakeFiles/diamond.dir/src/run/tools.cpp.o.d -o CMakeFiles/diamond.dir/src/run/tools.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/run/tools.cpp [ 22% 44/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/chaining/greedy_align.cpp.o -MF CMakeFiles/diamond.dir/src/chaining/greedy_align.cpp.o.d -o CMakeFiles/diamond.dir/src/chaining/greedy_align.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/chaining/greedy_align.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/chaining/greedy_align.cpp:32: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/chaining/../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/chaining/../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 23% 45/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/output/output_format.cpp.o -MF CMakeFiles/diamond.dir/src/output/output_format.cpp.o.d -o CMakeFiles/diamond.dir/src/output/output_format.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.cpp:27: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 23% 46/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/output/clustering_variables.cpp.o -MF CMakeFiles/diamond.dir/src/output/clustering_variables.cpp.o.d -o CMakeFiles/diamond.dir/src/output/clustering_variables.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/clustering_variables.cpp [ 24% 47/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/output/clustering_format.cpp.o -MF CMakeFiles/diamond.dir/src/output/clustering_format.cpp.o.d -o CMakeFiles/diamond.dir/src/output/clustering_format.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/clustering_format.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/clustering_format.cpp:20: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 25% 48/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/output/join_blocks.cpp.o -MF CMakeFiles/diamond.dir/src/output/join_blocks.cpp.o.d -o CMakeFiles/diamond.dir/src/output/join_blocks.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/join_blocks.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/join_blocks.cpp:25: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output.h:34: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 25% 49/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/data/frequent_seeds.cpp.o -MF CMakeFiles/diamond.dir/src/data/frequent_seeds.cpp.o.d -o CMakeFiles/diamond.dir/src/data/frequent_seeds.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/frequent_seeds.cpp [ 26% 50/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/align/legacy/query_mapper.cpp.o -MF CMakeFiles/diamond.dir/src/align/legacy/query_mapper.cpp.o.d -o CMakeFiles/diamond.dir/src/align/legacy/query_mapper.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/legacy/query_mapper.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/legacy/query_mapper.cpp:27: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/legacy/../../output/output.h:34: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/legacy/../../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/legacy/../../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 26% 51/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -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-2.1.9/src/output/blast_tab_format.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/blast_tab_format.cpp:30: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/blast_tab_format.cpp:216:16: warning: operator '?:' has lower precedence than '<<'; '<<' will be evaluated first [-Wparentheses] out << json ? ',': ';'; ~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/blast_tab_format.cpp:216:16: note: place parentheses around the '<<' expression to silence this warning out << json ? ',': ';'; ^ ( ) /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/blast_tab_format.cpp:216:16: note: place parentheses around the '?:' expression to evaluate it first out << json ? ',': ';'; ^ ( ) In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/blast_tab_format.cpp:33: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/../dp/../util/util.h:176:71: warning: 'result_of<(lambda at /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/blast_tab_format.cpp:656:50) (long)>' is deprecated [-Wdeprecated-declarations] auto apply(const std::vector &v, F f) -> std::vector::type> { ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of<(lambda at /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/blast_tab_format.cpp:656:50) (long)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/blast_tab_format.cpp:216:16: warning: operator '?:' has lower precedence than '<<'; '<<' will be evaluated first [-Wparentheses] out << json ? ',': ';'; ~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/blast_tab_format.cpp:370:4: note: in instantiation of function template specialization 'print_taxon_names>' requested here print_taxon_names(tax_id.begin(), tax_id.end(), *info.db, out, is_json); ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/blast_tab_format.cpp:216:16: note: place parentheses around the '<<' expression to silence this warning out << json ? ',': ';'; ^ ( ) /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/blast_tab_format.cpp:216:16: note: place parentheses around the '?:' expression to evaluate it first out << json ? ',': ';'; ^ ( ) /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/blast_tab_format.cpp:216:16: warning: operator '?:' has lower precedence than '<<'; '<<' will be evaluated first [-Wparentheses] out << json ? ',': ';'; ~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/blast_tab_format.cpp:375:4: note: in instantiation of function template specialization 'print_taxon_names *, long>>' requested here print_taxon_names(tax_id.begin(), tax_id.end(), *info.db, out, is_json); ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/blast_tab_format.cpp:216:16: note: place parentheses around the '<<' expression to silence this warning out << json ? ',': ';'; ^ ( ) /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/blast_tab_format.cpp:216:16: note: place parentheses around the '?:' expression to evaluate it first out << json ? ',': ';'; ^ ( ) 5 warnings generated. [ 27% 52/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/output/blast_pairwise_format.cpp.o -MF CMakeFiles/diamond.dir/src/output/blast_pairwise_format.cpp.o.d -o CMakeFiles/diamond.dir/src/output/blast_pairwise_format.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/blast_pairwise_format.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/blast_pairwise_format.cpp:19: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 27% 53/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/run/double_indexed.cpp.o -MF CMakeFiles/diamond.dir/src/run/double_indexed.cpp.o.d -o CMakeFiles/diamond.dir/src/run/double_indexed.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/run/double_indexed.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/run/double_indexed.cpp:36: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/run/../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/run/../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 28% 54/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/output/sam_format.cpp.o -MF CMakeFiles/diamond.dir/src/output/sam_format.cpp.o.d -o CMakeFiles/diamond.dir/src/output/sam_format.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/sam_format.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/sam_format.cpp:20: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 28% 55/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/align/align.cpp.o -MF CMakeFiles/diamond.dir/src/align/align.cpp.o.d -o CMakeFiles/diamond.dir/src/align/align.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/align.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/align.cpp:25: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 29% 56/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/search/setup.cpp.o -MF CMakeFiles/diamond.dir/src/search/setup.cpp.o.d -o CMakeFiles/diamond.dir/src/search/setup.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/search/setup.cpp [ 29% 57/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/data/taxonomy.cpp.o -MF CMakeFiles/diamond.dir/src/data/taxonomy.cpp.o.d -o CMakeFiles/diamond.dir/src/data/taxonomy.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/taxonomy.cpp [ 30% 58/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/masking/masking.cpp.o -MF CMakeFiles/diamond.dir/src/masking/masking.cpp.o.d -o CMakeFiles/diamond.dir/src/masking/masking.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/masking/masking.cpp [ 30% 59/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/data/seed_set.cpp.o -MF CMakeFiles/diamond.dir/src/data/seed_set.cpp.o.d -o CMakeFiles/diamond.dir/src/data/seed_set.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/seed_set.cpp [ 31% 60/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -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-2.1.9/src/util/simd.cpp [ 31% 61/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/output/taxon_format.cpp.o -MF CMakeFiles/diamond.dir/src/output/taxon_format.cpp.o.d -o CMakeFiles/diamond.dir/src/output/taxon_format.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/taxon_format.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/taxon_format.cpp:22: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 32% 62/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/output/daa/view.cpp.o -MF CMakeFiles/diamond.dir/src/output/daa/view.cpp.o.d -o CMakeFiles/diamond.dir/src/output/daa/view.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/daa/view.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/daa/view.cpp:30: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/daa/../output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/daa/../output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 32% 63/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/output/output_sink.cpp.o -MF CMakeFiles/diamond.dir/src/output/output_sink.cpp.o.d -o CMakeFiles/diamond.dir/src/output/output_sink.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_sink.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_sink.cpp:21: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output.h:34: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 33% 64/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/output/target_culling.cpp.o -MF CMakeFiles/diamond.dir/src/output/target_culling.cpp.o.d -o CMakeFiles/diamond.dir/src/output/target_culling.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/target_culling.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/target_culling.cpp:19: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/target_culling.h:28: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output.h:34: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 33% 65/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/align/legacy/banded_swipe_pipeline.cpp.o -MF CMakeFiles/diamond.dir/src/align/legacy/banded_swipe_pipeline.cpp.o.d -o CMakeFiles/diamond.dir/src/align/legacy/banded_swipe_pipeline.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/legacy/banded_swipe_pipeline.cpp [ 34% 66/192] /ccache/libexec/ccache/c++ -DLEFTMOST_SEED_FILTER 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-I/wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/util/io/deserializer.cpp.o -MF CMakeFiles/diamond.dir/src/util/io/deserializer.cpp.o.d -o CMakeFiles/diamond.dir/src/util/io/deserializer.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/util/io/deserializer.cpp [ 35% 68/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/util/io/file_sink.cpp.o -MF CMakeFiles/diamond.dir/src/util/io/file_sink.cpp.o.d -o CMakeFiles/diamond.dir/src/util/io/file_sink.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/util/io/file_sink.cpp [ 35% 69/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -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-2.1.9/src/util/io/file_source.cpp [ 36% 70/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe 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-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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/util/io/temp_file.cpp.o -MF CMakeFiles/diamond.dir/src/util/io/temp_file.cpp.o.d -o CMakeFiles/diamond.dir/src/util/io/temp_file.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/util/io/temp_file.cpp [ 39% 76/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/util/io/text_input_file.cpp.o -MF CMakeFiles/diamond.dir/src/util/io/text_input_file.cpp.o.d -o CMakeFiles/diamond.dir/src/util/io/text_input_file.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/util/io/text_input_file.cpp [ 40% 77/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/data/taxon_list.cpp.o -MF CMakeFiles/diamond.dir/src/data/taxon_list.cpp.o.d -o CMakeFiles/diamond.dir/src/data/taxon_list.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/taxon_list.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/taxon_list.cpp:31: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/../util/algo/sort_helper.h:39:16: warning: 'result_of<(lambda at /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/taxon_list.cpp:114:21) (const std::pair &, const std::pair &)>' is deprecated [-Wdeprecated-declarations] typename std::result_of::type operator*() const { ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/taxon_list.cpp:115:12: note: in instantiation of template class 'SortedListJoiner, std::less>>, ExternalSorter>, First, First, (lambda at /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/taxon_list.cpp:114:21)>' requested here auto it = join_sorted_lists(acc2oid, acc2taxid, First(), First(), value); ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of<(lambda at /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/taxon_list.cpp:114:21) (const std::pair &, const std::pair &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/taxon_list.cpp:31: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/../util/algo/sort_helper.h:125:82: warning: 'result_of (const std::pair &)>' is deprecated [-Wdeprecated-declarations] KeyMerger merge_keys(It& it, Key key, Value value, typename std::result_of::type begin) { ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of (const std::pair &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/taxon_list.cpp:31: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/../util/algo/sort_helper.h:91:24: warning: 'result_of (const std::pair &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::type KeyType; ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/taxon_list.cpp:128:18: note: in instantiation of template class 'KeyMerger>, First, Second>' requested here auto taxid_it = merge_keys(oid2taxid, First(), Second(), 0); ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of (const std::pair &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/taxon_list.cpp:31: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/../util/algo/sort_helper.h:92:24: warning: 'result_of (const std::pair &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::type ValueType; ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of (const std::pair &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ 4 warnings generated. [ 40% 78/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/data/taxonomy_nodes.cpp.o -MF CMakeFiles/diamond.dir/src/data/taxonomy_nodes.cpp.o.d -o CMakeFiles/diamond.dir/src/data/taxonomy_nodes.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/taxonomy_nodes.cpp [ 41% 79/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/util/algo/MurmurHash3.cpp.o -MF CMakeFiles/diamond.dir/src/util/algo/MurmurHash3.cpp.o.d -o CMakeFiles/diamond.dir/src/util/algo/MurmurHash3.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/util/algo/MurmurHash3.cpp [ 41% 80/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/search/stage0.cpp.o -MF CMakeFiles/diamond.dir/src/search/stage0.cpp.o.d -o CMakeFiles/diamond.dir/src/search/stage0.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/search/stage0.cpp [ 42% 81/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/data/seed_array.cpp.o -MF CMakeFiles/diamond.dir/src/data/seed_array.cpp.o.d -o CMakeFiles/diamond.dir/src/data/seed_array.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/seed_array.cpp [ 42% 82/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/output/paf_format.cpp.o -MF CMakeFiles/diamond.dir/src/output/paf_format.cpp.o.d -o CMakeFiles/diamond.dir/src/output/paf_format.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/paf_format.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/paf_format.cpp:19: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 43% 83/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/util/system/system.cpp.o -MF CMakeFiles/diamond.dir/src/util/system/system.cpp.o.d -o CMakeFiles/diamond.dir/src/util/system/system.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/util/system/system.cpp [ 43% 84/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/util/algo/greedy_vertex_cover.cpp.o -MF CMakeFiles/diamond.dir/src/util/algo/greedy_vertex_cover.cpp.o.d -o CMakeFiles/diamond.dir/src/util/algo/greedy_vertex_cover.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/util/algo/greedy_vertex_cover.cpp [ 44% 85/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/util/sequence/sequence.cpp.o -MF CMakeFiles/diamond.dir/src/util/sequence/sequence.cpp.o.d -o CMakeFiles/diamond.dir/src/util/sequence/sequence.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/util/sequence/sequence.cpp [ 44% 86/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/tools/tsv_record.cpp.o -MF CMakeFiles/diamond.dir/src/tools/tsv_record.cpp.o.d -o CMakeFiles/diamond.dir/src/tools/tsv_record.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/tsv_record.cpp [ 45% 87/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -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-2.1.9/src/tools/tools.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/tools.cpp:9: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/../data/../util/data_structures/../util.h:224:24: warning: 'result_of<(lambda at /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/tools.cpp:143:51) (unsigned long &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::type KeyType; ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/tools.cpp:143:12: note: in instantiation of template class 'KeyMergeIterator, (lambda at /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/tools.cpp:143:51)>' requested here auto it = merge_keys(seeds.begin(), seeds.end(), [](uint64_t seed) {return seed; }); ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of<(lambda at /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/tools.cpp:143:51) (unsigned long &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ 1 warning generated. [ 45% 88/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/util/system/getRSS.cpp.o -MF CMakeFiles/diamond.dir/src/util/system/getRSS.cpp.o.d -o CMakeFiles/diamond.dir/src/util/system/getRSS.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/util/system/getRSS.cpp [ 46% 89/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/lib/tantan/LambdaCalculator.cc.o -MF CMakeFiles/diamond.dir/src/lib/tantan/LambdaCalculator.cc.o.d -o CMakeFiles/diamond.dir/src/lib/tantan/LambdaCalculator.cc.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib/tantan/LambdaCalculator.cc [ 46% 90/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/util/algo/edge_vec.cpp.o -MF CMakeFiles/diamond.dir/src/util/algo/edge_vec.cpp.o.d -o CMakeFiles/diamond.dir/src/util/algo/edge_vec.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/util/algo/edge_vec.cpp [ 47% 91/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/util/string/string.cpp.o -MF CMakeFiles/diamond.dir/src/util/string/string.cpp.o.d -o CMakeFiles/diamond.dir/src/util/string/string.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/util/string/string.cpp [ 47% 92/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/align/extend.cpp.o -MF CMakeFiles/diamond.dir/src/align/extend.cpp.o.d -o CMakeFiles/diamond.dir/src/align/extend.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/extend.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/extend.cpp:36: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/global_ranking.h:21: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/../../output/output.h:34: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 48% 93/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/test/test.cpp.o -MF CMakeFiles/diamond.dir/src/test/test.cpp.o.d -o CMakeFiles/diamond.dir/src/test/test.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/test/test.cpp [ 48% 94/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/align/ungapped.cpp.o -MF CMakeFiles/diamond.dir/src/align/ungapped.cpp.o.d -o CMakeFiles/diamond.dir/src/align/ungapped.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/ungapped.cpp [ 49% 95/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/align/gapped_score.cpp.o -MF CMakeFiles/diamond.dir/src/align/gapped_score.cpp.o.d -o CMakeFiles/diamond.dir/src/align/gapped_score.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/gapped_score.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/gapped_score.cpp:28: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 50% 96/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/align/gapped_final.cpp.o -MF CMakeFiles/diamond.dir/src/align/gapped_final.cpp.o.d -o CMakeFiles/diamond.dir/src/align/gapped_final.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/gapped_final.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/gapped_final.cpp:4: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 50% 97/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/align/full_db.cpp.o -MF CMakeFiles/diamond.dir/src/align/full_db.cpp.o.d -o CMakeFiles/diamond.dir/src/align/full_db.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/full_db.cpp [ 51% 98/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/align/culling.cpp.o -MF CMakeFiles/diamond.dir/src/align/culling.cpp.o.d -o CMakeFiles/diamond.dir/src/align/culling.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/culling.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/culling.cpp:26: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 51% 99/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/cluster/cluster_registry.cpp.o -MF CMakeFiles/diamond.dir/src/cluster/cluster_registry.cpp.o.d -o CMakeFiles/diamond.dir/src/cluster/cluster_registry.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cluster_registry.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cluster_registry.cpp:20: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cluster_registry.h:21: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cluster.h:28: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 52% 100/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/cluster/cascaded/cascaded.cpp.o -MF CMakeFiles/diamond.dir/src/cluster/cascaded/cascaded.cpp.o.d -o CMakeFiles/diamond.dir/src/cluster/cascaded/cascaded.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/cascaded.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/cascaded.cpp:23: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/cascaded.h:23: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/../cluster.h:28: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/../../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/../../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/cascaded.cpp:23: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/cascaded.h:23: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/../cluster.h:25: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/../../data/../util/io/../algo/../data_structures/flat_array.h:28: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib/../util/util.h:224:24: warning: 'result_of::GetKey (Util::Algo::Edge &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::type KeyType; ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/../../data/../util/io/../algo/../data_structures/flat_array.h:288:12: note: in instantiation of template class 'KeyMergeIterator *>, Util::Algo::Edge::GetKey>' requested here auto it = merge_keys(data.cbegin(), data.cend(), get_key); ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/cascaded.cpp:102:31: note: in instantiation of function template specialization 'make_flat_array_dense, Util::Algo::Edge::GetKey>' requested here FlatArray edge_array = make_flat_array_dense(move(edges), (SuperBlockId)db->sequence_count(), config.threads_, Edge::GetKey()); ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of::GetKey (Util::Algo::Edge &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ 2 warnings generated. [ 52% 101/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/align/output.cpp.o -MF CMakeFiles/diamond.dir/src/align/output.cpp.o.d -o CMakeFiles/diamond.dir/src/align/output.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/output.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/output.cpp:25: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 53% 102/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/tools/roc.cpp.o -MF CMakeFiles/diamond.dir/src/tools/roc.cpp.o.d -o CMakeFiles/diamond.dir/src/tools/roc.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/roc.cpp [ 53% 103/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/test/data.cpp.o -MF CMakeFiles/diamond.dir/src/test/data.cpp.o.d -o CMakeFiles/diamond.dir/src/test/data.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/test/data.cpp [ 54% 104/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/test/test_cases.cpp.o -MF CMakeFiles/diamond.dir/src/test/test_cases.cpp.o.d -o CMakeFiles/diamond.dir/src/test/test_cases.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/test/test_cases.cpp [ 54% 105/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/chaining/smith_waterman.cpp.o -MF CMakeFiles/diamond.dir/src/chaining/smith_waterman.cpp.o.d -o CMakeFiles/diamond.dir/src/chaining/smith_waterman.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/chaining/smith_waterman.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/chaining/smith_waterman.cpp:3: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/chaining/../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/chaining/../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 55% 106/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/output/xml_format.cpp.o -MF CMakeFiles/diamond.dir/src/output/xml_format.cpp.o.d -o CMakeFiles/diamond.dir/src/output/xml_format.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/xml_format.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/xml_format.cpp:2: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. 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function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/../../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. 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CMakeFiles/diamond.dir/src/stats/hauser_correction.cpp.o.d -o CMakeFiles/diamond.dir/src/stats/hauser_correction.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/hauser_correction.cpp [ 75% 145/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/stats/matrix_adjust.cpp.o -MF CMakeFiles/diamond.dir/src/stats/matrix_adjust.cpp.o.d -o CMakeFiles/diamond.dir/src/stats/matrix_adjust.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/matrix_adjust.cpp [ 76% 146/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/stats/matrix_adjust_eigen.cpp.o -MF CMakeFiles/diamond.dir/src/stats/matrix_adjust_eigen.cpp.o.d -o CMakeFiles/diamond.dir/src/stats/matrix_adjust_eigen.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/matrix_adjust_eigen.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/matrix_adjust_eigen.cpp:22: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/Core:367: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of (const float &, const float &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::type type1; ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of (const float &, const float &)>' requested here typedef typename result_of< ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits, const Eigen::PartialReduxExpr, Eigen::internal::member_sum, 0>, const Eigen::CwiseNullaryOp, const Eigen::Matrix>>>' requested here template::XprKind, typename StorageKind = typename traits::StorageKind> ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base, const Eigen::PartialReduxExpr, Eigen::internal::member_sum, 0>, const Eigen::CwiseNullaryOp, const Eigen::Matrix>>>' required here : public internal::generic_xpr_base >::type ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl, const Eigen::PartialReduxExpr, Eigen::internal::member_sum, 0>, const Eigen::CwiseNullaryOp, const Eigen::Matrix>, Eigen::Dense>' requested here public CwiseBinaryOpImpl< ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/matrix_adjust_eigen.cpp:106:36: note: in instantiation of template class 'Eigen::CwiseBinaryOp, const Eigen::PartialReduxExpr, Eigen::internal::member_sum, 0>, const Eigen::CwiseNullaryOp, const Eigen::Matrix>>' requested here VectorN sc = x.colwise().sum() * alpha, sr = x.rowwise().sum() * alpha; ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of (const float &, const float &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/matrix_adjust_eigen.cpp:22: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/Core:367: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of (const float &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::type type1; ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseUnaryOp.h:21:20: note: in instantiation of template class 'Eigen::internal::result_of (const float &)>' requested here typedef typename result_of< ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits, const Eigen::Block, 1, 400, true>>>' requested here template::XprKind, typename StorageKind = typename traits::StorageKind> ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseUnaryOp.h:95:22: note: in instantiation of default argument for 'generic_xpr_base, const Eigen::Block, 1, 400, true>>>' required here : public internal::generic_xpr_base >::type ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseUnaryOp.h:55:29: note: in instantiation of template class 'Eigen::CwiseUnaryOpImpl, const Eigen::Block, 1, 400, true>, Eigen::Dense>' requested here class CwiseUnaryOp : public CwiseUnaryOpImpl::StorageKind>, internal::no_assignment_operator ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/matrix_adjust_eigen.cpp:156:18: note: in instantiation of template class 'Eigen::CwiseUnaryOp, const Eigen::Block, 1, 400, true>>' requested here VectorNN v = -grads.row(0) + eta * grads.row(1); ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of (const float &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/matrix_adjust_eigen.cpp:22: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/Core:367: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of (const float &, const float &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::type type1; ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of (const float &, const float &)>' requested here typedef typename result_of< ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits, const Eigen::CwiseUnaryOp, const Eigen::Block, 1, 400, true>>, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix>, const Eigen::Block, 1, 400, true>>>>' requested here template::XprKind, typename StorageKind = typename traits::StorageKind> ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base, const Eigen::CwiseUnaryOp, const Eigen::Block, 1, 400, true>>, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix>, const Eigen::Block, 1, 400, true>>>>' required here : public internal::generic_xpr_base >::type ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl, const Eigen::CwiseUnaryOp, const Eigen::Block, 1, 400, true>>, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix>, const Eigen::Block, 1, 400, true>>, Eigen::Dense>' requested here public CwiseBinaryOpImpl< ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/matrix_adjust_eigen.cpp:156:32: note: in instantiation of template class 'Eigen::CwiseBinaryOp, const Eigen::CwiseUnaryOp, const Eigen::Block, 1, 400, true>>, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix>, const Eigen::Block, 1, 400, true>>>' requested here VectorNN v = -grads.row(0) + eta * grads.row(1); ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of (const float &, const float &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/matrix_adjust_eigen.cpp:22: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/Core:367: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of (const float &, const float &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::type type1; ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of (const float &, const float &)>' requested here typedef typename result_of< ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits, const Eigen::ArrayWrapper>, const Eigen::ArrayWrapper>>>' requested here template::XprKind, typename StorageKind = typename traits::StorageKind> ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base, const Eigen::ArrayWrapper>, const Eigen::ArrayWrapper>>>' required here : public internal::generic_xpr_base >::type ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl, const Eigen::ArrayWrapper>, const Eigen::ArrayWrapper>, Eigen::Dense>' requested here public CwiseBinaryOpImpl< ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/matrix_adjust_eigen.cpp:306:30: note: in instantiation of template class 'Eigen::CwiseBinaryOp, const Eigen::ArrayWrapper>, const Eigen::ArrayWrapper>>' requested here MatrixN tmp = (x.array() / q.array()).log(); ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of (const float &, const float &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/matrix_adjust_eigen.cpp:22: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/Core:367: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of (const float &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::type type1; ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseUnaryOp.h:21:20: note: in instantiation of template class 'Eigen::internal::result_of (const float &)>' requested here typedef typename result_of< ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits, const Eigen::CwiseBinaryOp, const Eigen::ArrayWrapper>, const Eigen::ArrayWrapper>>>>' requested here template::XprKind, typename StorageKind = typename traits::StorageKind> ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseUnaryOp.h:95:22: note: in instantiation of default argument for 'generic_xpr_base, const Eigen::CwiseBinaryOp, const Eigen::ArrayWrapper>, const Eigen::ArrayWrapper>>>>' required here : public internal::generic_xpr_base >::type ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseUnaryOp.h:55:29: note: in instantiation of template class 'Eigen::CwiseUnaryOpImpl, const Eigen::CwiseBinaryOp, const Eigen::ArrayWrapper>, const Eigen::ArrayWrapper>>, Eigen::Dense>' requested here class CwiseUnaryOp : public CwiseUnaryOpImpl::StorageKind>, internal::no_assignment_operator ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/matrix_adjust_eigen.cpp:306:43: note: in instantiation of template class 'Eigen::CwiseUnaryOp, const Eigen::CwiseBinaryOp, const Eigen::ArrayWrapper>, const Eigen::ArrayWrapper>>>' requested here MatrixN tmp = (x.array() / q.array()).log(); ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of (const float &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/matrix_adjust_eigen.cpp:22: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/Core:367: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of (const float &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::type type1; ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseUnaryOp.h:21:20: note: in instantiation of template class 'Eigen::internal::result_of (const float &)>' requested here typedef typename result_of< ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits, const Eigen::Matrix>>' requested here template::XprKind, typename StorageKind = typename traits::StorageKind> ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseUnaryOp.h:95:22: note: in instantiation of default argument for 'generic_xpr_base, const Eigen::Matrix>>' required here : public internal::generic_xpr_base >::type ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseUnaryOp.h:55:29: note: in instantiation of template class 'Eigen::CwiseUnaryOpImpl, const Eigen::Matrix, Eigen::Dense>' requested here class CwiseUnaryOp : public CwiseUnaryOpImpl::StorageKind>, internal::no_assignment_operator ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/Dot.h:98:31: note: in instantiation of template class 'Eigen::CwiseUnaryOp, const Eigen::Matrix>' requested here return numext::real((*this).cwiseAbs2().sum()); ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/Dot.h:110:23: note: in instantiation of member function 'Eigen::MatrixBase>::squaredNorm' requested here return numext::sqrt(squaredNorm()); ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/matrix_adjust_eigen.cpp:179:27: note: in instantiation of member function 'Eigen::MatrixBase>::norm' requested here norm_resids_x = resids_x.norm(); ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of (const float &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/matrix_adjust_eigen.cpp:22: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/Core:367: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of (const float &, const float &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::type type1; ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of (const float &, const float &)>' requested here typedef typename result_of< ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits, const Eigen::Block, 1, 20, true>, const Eigen::Block, 1, 20, false>>>' requested here template::XprKind, typename StorageKind = typename traits::StorageKind> ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base, const Eigen::Block, 1, 20, true>, const Eigen::Block, 1, 20, false>>>' required here : public internal::generic_xpr_base >::type ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl, const Eigen::Block, 1, 20, true>, const Eigen::Block, 1, 20, false>, Eigen::Dense>' requested here public CwiseBinaryOpImpl< ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/Dot.h:37:23: note: in instantiation of template class 'Eigen::CwiseBinaryOp, const Eigen::Block, 1, 20, true>, const Eigen::Block, 1, 20, false>>' requested here return a.template binaryExpr(b).sum(); ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/Dot.h:84:55: note: in instantiation of member function 'Eigen::internal::dot_nocheck, 1, 20, true>, Eigen::Block, 1, 20, false>, false>::run' requested here return internal::dot_nocheck::run(*this, other); ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/matrix_adjust_eigen.cpp:249:45: note: in instantiation of function template specialization 'Eigen::MatrixBase, 1, 20, true>>::dot, 1, 20, false>>' requested here W(m - 1, m - 1) += workspace.row(i).dot(grad_re.segment(i * N)); ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of (const float &, const float &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/matrix_adjust_eigen.cpp:22: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/Core:367: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of (const float &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::type type1; ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseUnaryOp.h:21:20: note: in instantiation of template class 'Eigen::internal::result_of (const float &)>' requested here typedef typename result_of< ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits, const Eigen::Block, 40, 1, false>, -1, 1, false>>>' requested here template::XprKind, typename StorageKind = typename traits::StorageKind> ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseUnaryOp.h:95:22: note: in instantiation of default argument for 'generic_xpr_base, const Eigen::Block, 40, 1, false>, -1, 1, false>>>' required here : public internal::generic_xpr_base >::type ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/CwiseUnaryOp.h:55:29: note: in instantiation of template class 'Eigen::CwiseUnaryOpImpl, const Eigen::Block, 40, 1, false>, -1, 1, false>, Eigen::Dense>' requested here class CwiseUnaryOp : public CwiseUnaryOpImpl::StorageKind>, internal::no_assignment_operator ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/Dot.h:221:14: note: in instantiation of template class 'Eigen::CwiseUnaryOp, const Eigen::Block, 40, 1, false>, -1, 1, false>>' requested here return m.cwiseAbs().sum(); ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Core/Dot.h:269:49: note: in instantiation of member function 'Eigen::internal::lpNorm_selector, 40, 1, false>, -1, 1, false>, 1>::run' requested here return internal::lpNorm_selector::run(*this); ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Cholesky/LLT.h:441:65: note: in instantiation of function template specialization 'Eigen::MatrixBase, 40, 1, false>, -1, 1, false>>::lpNorm<1>' requested here abs_col_sum = m_matrix.col(col).tail(size - col).template lpNorm<1>() + m_matrix.row(col).head(col).template lpNorm<1>(); ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Cholesky/LLT.h:100:7: note: in instantiation of function template specialization 'Eigen::LLT, 1>::compute>' requested here compute(matrix.derived()); ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/../lib/Eigen/src/Cholesky/LLT.h:526:10: note: in instantiation of function template specialization 'Eigen::LLT, 1>::LLT>' requested here return LLT(derived()); ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/matrix_adjust_eigen.cpp:287:11: note: in instantiation of member function 'Eigen::MatrixBase>::llt' requested here z = W.llt().solve(z); ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of (const float &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ 8 warnings generated. [ 76% 147/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/data/index.cpp.o -MF CMakeFiles/diamond.dir/src/data/index.cpp.o.d -o CMakeFiles/diamond.dir/src/data/index.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/index.cpp [ 77% 148/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -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-2.1.9/src/data/dmnd/dmnd.cpp [ 77% 149/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -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-2.1.9/src/data/sequence_file.cpp [ 78% 150/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/tools/find_shapes.cpp.o -MF CMakeFiles/diamond.dir/src/tools/find_shapes.cpp.o.d -o CMakeFiles/diamond.dir/src/tools/find_shapes.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/find_shapes.cpp [ 78% 151/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -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-2.1.9/src/data/block/block.cpp [ 79% 152/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/data/block/block_wrapper.cpp.o -MF CMakeFiles/diamond.dir/src/data/block/block_wrapper.cpp.o.d -o CMakeFiles/diamond.dir/src/data/block/block_wrapper.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/block/block_wrapper.cpp [ 79% 153/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/run/config.cpp.o -MF CMakeFiles/diamond.dir/src/run/config.cpp.o.d -o CMakeFiles/diamond.dir/src/run/config.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/run/config.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/run/config.cpp:10: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/run/../align/global_ranking/global_ranking.h:21: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/run/../align/global_ranking/../../output/output.h:34: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/run/../align/global_ranking/../../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/run/../align/global_ranking/../../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 80% 154/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/data/sequence_set.cpp.o -MF CMakeFiles/diamond.dir/src/data/sequence_set.cpp.o.d -o CMakeFiles/diamond.dir/src/data/sequence_set.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/sequence_set.cpp [ 80% 155/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -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-2.1.9/src/align/global_ranking/table.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/table.cpp:21: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/global_ranking.h:21: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/../../output/output.h:34: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/../../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/../../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/table.cpp:21: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/global_ranking.h:25: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/../target.h:35: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/../../search/../util/data_structures/flat_array.h:28: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/../../util/util.h:224:24: warning: 'result_of<(lambda at /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/table.cpp:50:21) (Search::Hit &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::type KeyType; ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/table.cpp:51:13: note: in instantiation of template class 'KeyMergeIterator::Iterator, (lambda at /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/table.cpp:50:21)>' requested here auto it = merge_keys(begin, end, get_target); ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of<(lambda at /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/table.cpp:50:21) (Search::Hit &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/table.cpp:21: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/global_ranking.h:25: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/../target.h:35: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/../../search/../util/data_structures/flat_array.h:28: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/../../util/util.h:224:24: warning: 'result_of<(lambda at /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/table.cpp:77:21) (Search::Hit &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::type KeyType; ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/table.cpp:78:13: note: in instantiation of template class 'KeyMergeIterator::Iterator, (lambda at /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/table.cpp:77:21)>' requested here auto it = merge_keys(begin, end, get_target); ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of<(lambda at /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/table.cpp:77:21) (Search::Hit &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/table.cpp:21: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/global_ranking.h:25: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/../target.h:35: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/../../search/../util/data_structures/flat_array.h:28: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/../../util/util.h:224:24: warning: 'result_of' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::type KeyType; ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/global_ranking/table.cpp:174:14: note: in instantiation of template class 'KeyMergeIterator::Iterator, Search::Hit::SourceQuery>' requested here auto it = merge_keys(begin, end, ::Search::Hit::SourceQuery{ align_mode.query_contexts }); ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ 4 warnings generated. [ 81% 156/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/output/daa/daa_write.cpp.o -MF CMakeFiles/diamond.dir/src/output/daa/daa_write.cpp.o.d -o CMakeFiles/diamond.dir/src/output/daa/daa_write.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/daa/daa_write.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/daa/daa_write.cpp:1: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/daa/daa_write.h:24: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/daa/../output.h:34: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/daa/../output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/daa/../output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 81% 157/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/search/seed_complexity.cpp.o -MF CMakeFiles/diamond.dir/src/search/seed_complexity.cpp.o.d -o CMakeFiles/diamond.dir/src/search/seed_complexity.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/search/seed_complexity.cpp [ 82% 158/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/tools/view.cpp.o -MF CMakeFiles/diamond.dir/src/tools/view.cpp.o.d -o CMakeFiles/diamond.dir/src/tools/view.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/view.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/view.cpp:9: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 82% 159/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/util/tsv/tsv.cpp.o -MF CMakeFiles/diamond.dir/src/util/tsv/tsv.cpp.o.d -o CMakeFiles/diamond.dir/src/util/tsv/tsv.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/util/tsv/tsv.cpp [ 83% 160/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/tools/join.cpp.o -MF CMakeFiles/diamond.dir/src/tools/join.cpp.o.d -o CMakeFiles/diamond.dir/src/tools/join.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/join.cpp [ 83% 161/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/basic/value.cpp.o -MF CMakeFiles/diamond.dir/src/basic/value.cpp.o.d -o CMakeFiles/diamond.dir/src/basic/value.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/basic/value.cpp [ 84% 162/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/masking/motifs.cpp.o -MF CMakeFiles/diamond.dir/src/masking/motifs.cpp.o.d -o CMakeFiles/diamond.dir/src/masking/motifs.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/masking/motifs.cpp [ 84% 163/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/align/alt_hsp.cpp.o -MF CMakeFiles/diamond.dir/src/align/alt_hsp.cpp.o.d -o CMakeFiles/diamond.dir/src/align/alt_hsp.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/align/alt_hsp.cpp [ 85% 164/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/data/fasta/fasta_file.cpp.o -MF CMakeFiles/diamond.dir/src/data/fasta/fasta_file.cpp.o.d -o CMakeFiles/diamond.dir/src/data/fasta/fasta_file.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/data/fasta/fasta_file.cpp [ 85% 165/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/cluster/output.cpp.o -MF CMakeFiles/diamond.dir/src/cluster/output.cpp.o.d -o CMakeFiles/diamond.dir/src/cluster/output.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/output.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/output.cpp:23: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cluster.h:28: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 86% 166/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -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-2.1.9/src/cluster/realign.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/realign.cpp:26: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cluster.h:28: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 86% 167/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/cluster/reassign.cpp.o -MF CMakeFiles/diamond.dir/src/cluster/reassign.cpp.o.d -o CMakeFiles/diamond.dir/src/cluster/reassign.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/reassign.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/reassign.cpp:23: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cluster.h:28: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 87% 168/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/util/tsv/read_tsv.cpp.o -MF CMakeFiles/diamond.dir/src/util/tsv/read_tsv.cpp.o.d -o CMakeFiles/diamond.dir/src/util/tsv/read_tsv.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/util/tsv/read_tsv.cpp [ 88% 169/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -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-2.1.9/src/tools/greedy_vertex_cover.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/greedy_vertex_cover.cpp:34: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/../cluster/cluster.h:28: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/../cluster/../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/../cluster/../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/greedy_vertex_cover.cpp:32: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/../cluster/../util/algo/algo.h:8: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/../cluster/../util/data_structures/flat_array.h:28: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/../util/tsv/../io/../algo/../data_structures/../util.h:224:24: warning: 'result_of::GetKey (Util::Algo::Edge &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::type KeyType; ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/../cluster/../util/data_structures/flat_array.h:288:12: note: in instantiation of template class 'KeyMergeIterator *>, Util::Algo::Edge::GetKey>' requested here auto it = merge_keys(data.cbegin(), data.cend(), get_key); ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/tools/greedy_vertex_cover.cpp:151:31: note: in instantiation of function template specialization 'make_flat_array_dense, Util::Algo::Edge::GetKey>' requested here FlatArray edge_array = make_flat_array_dense(move(edges), (Int)acc2oid.size(), config.threads_, Edge::GetKey()); ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of::GetKey (Util::Algo::Edge &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ 2 warnings generated. [ 88% 170/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/cluster/cascaded/recluster.cpp.o -MF CMakeFiles/diamond.dir/src/cluster/cascaded/recluster.cpp.o.d -o CMakeFiles/diamond.dir/src/cluster/cascaded/recluster.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/recluster.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/recluster.cpp:21: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/cascaded.h:23: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/../cluster.h:28: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/../../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/../../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 89% 171/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -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-2.1.9/src/cluster/helpers.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/helpers.cpp:23: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cluster.h:28: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/helpers.cpp:23: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cluster.h:25: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/../search/../util/data_structures/flat_array.h:28: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/../data/../util/data_structures/../util.h:224:24: warning: 'result_of (std::pair &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::type KeyType; ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/../search/../util/data_structures/flat_array.h:231:12: note: in instantiation of template class 'KeyMergeIterator *>, First>' requested here auto it = merge_keys(begin, end, First()); ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/helpers.cpp:73:9: note: in instantiation of function template specialization 'make_flat_array *>>' requested here return make_flat_array(pairs.begin(), pairs.end(), config.threads_); ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of (std::pair &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/helpers.cpp:23: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cluster.h:25: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/../search/../util/data_structures/flat_array.h:27: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/../data/../util/data_structures/../algo/transform_iterator.h:8:34: warning: 'result_of (const std::pair &)>' is deprecated [-Wdeprecated-declarations] using reference = typename std::result_of::type; ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/../search/../util/data_structures/flat_array.h:243:21: note: in instantiation of template class 'TransformIterator *>, Second>' requested here r.first.push_back(transform(it2.begin(), Second()), transform(it2.end(), Second())); ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/helpers.cpp:73:9: note: in instantiation of function template specialization 'make_flat_array *>>' requested here return make_flat_array(pairs.begin(), pairs.end(), config.threads_); ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of (const std::pair &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/helpers.cpp:23: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cluster.h:25: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/../search/../util/data_structures/flat_array.h:28: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/../data/../util/data_structures/../util.h:224:24: warning: 'result_of (std::pair &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::type KeyType; ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/../search/../util/data_structures/flat_array.h:231:12: note: in instantiation of template class 'KeyMergeIterator *>, First>' requested here auto it = merge_keys(begin, end, First()); ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/helpers.cpp:73:9: note: in instantiation of function template specialization 'make_flat_array *>>' requested here return make_flat_array(pairs.begin(), pairs.end(), config.threads_); ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of (std::pair &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/helpers.cpp:23: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cluster.h:25: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/../search/../util/data_structures/flat_array.h:27: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/../data/../util/data_structures/../algo/transform_iterator.h:8:34: warning: 'result_of (const std::pair &)>' is deprecated [-Wdeprecated-declarations] using reference = typename std::result_of::type; ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/../search/../util/data_structures/flat_array.h:243:21: note: in instantiation of template class 'TransformIterator *>, Second>' requested here r.first.push_back(transform(it2.begin(), Second()), transform(it2.end(), Second())); ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/helpers.cpp:73:9: note: in instantiation of function template specialization 'make_flat_array *>>' requested here return make_flat_array(pairs.begin(), pairs.end(), config.threads_); ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of (const std::pair &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ 5 warnings generated. [ 89% 172/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/search/kmer_ranking.cpp.o -MF CMakeFiles/diamond.dir/src/search/kmer_ranking.cpp.o.d -o CMakeFiles/diamond.dir/src/search/kmer_ranking.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/search/kmer_ranking.cpp [ 90% 173/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/chaining/hamming_ext.cpp.o -MF CMakeFiles/diamond.dir/src/chaining/hamming_ext.cpp.o.d -o CMakeFiles/diamond.dir/src/chaining/hamming_ext.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/chaining/hamming_ext.cpp [ 90% 174/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/dna/smith_watermann.cpp.o -MF CMakeFiles/diamond.dir/src/dna/smith_watermann.cpp.o.d -o CMakeFiles/diamond.dir/src/dna/smith_watermann.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/dna/smith_watermann.cpp [ 91% 175/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/stats/dna_scoring/build_score.cpp.o -MF CMakeFiles/diamond.dir/src/stats/dna_scoring/build_score.cpp.o.d -o CMakeFiles/diamond.dir/src/stats/dna_scoring/build_score.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/stats/dna_scoring/build_score.cpp [ 91% 176/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/lib/blast/blast_message.cpp.o -MF CMakeFiles/diamond.dir/src/lib/blast/blast_message.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/blast/blast_message.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib/blast/blast_message.cpp [ 92% 177/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/lib/blast/blast_stat.cpp.o -MF CMakeFiles/diamond.dir/src/lib/blast/blast_stat.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/blast/blast_stat.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib/blast/blast_stat.cpp [ 92% 178/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/lib/blast/blastn_score.cpp.o -MF CMakeFiles/diamond.dir/src/lib/blast/blastn_score.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/blast/blastn_score.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib/blast/blastn_score.cpp /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib/blast/blastn_score.cpp:442:37: warning: array subscript is of type 'char' [-Wchar-subscripts] x_index = AMINOACID_TO_NCBISTDAA['X']; ^~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib/blast/blastn_score.cpp:443:37: warning: array subscript is of type 'char' [-Wchar-subscripts] u_index = AMINOACID_TO_NCBISTDAA['U']; ^~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib/blast/blastn_score.cpp:444:37: warning: array subscript is of type 'char' [-Wchar-subscripts] o_index = AMINOACID_TO_NCBISTDAA['O']; ^~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib/blast/blastn_score.cpp:445:37: warning: array subscript is of type 'char' [-Wchar-subscripts] c_index = AMINOACID_TO_NCBISTDAA['C']; ^~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib/blast/blastn_score.cpp:929:48: warning: array subscript is of type 'char' [-Wchar-subscripts] if (i == AMINOACID_TO_NCBISTDAA['U'] || ^~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib/blast/blastn_score.cpp:930:48: warning: array subscript is of type 'char' [-Wchar-subscripts] i == AMINOACID_TO_NCBISTDAA['O'] || ^~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib/blast/blastn_score.cpp:931:48: warning: array subscript is of type 'char' [-Wchar-subscripts] i == AMINOACID_TO_NCBISTDAA['-'] || ^~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib/blast/blastn_score.cpp:932:48: warning: array subscript is of type 'char' [-Wchar-subscripts] j == AMINOACID_TO_NCBISTDAA['U'] || ^~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib/blast/blastn_score.cpp:933:48: warning: array subscript is of type 'char' [-Wchar-subscripts] j == AMINOACID_TO_NCBISTDAA['O'] || ^~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib/blast/blastn_score.cpp:934:48: warning: array subscript is of type 'char' [-Wchar-subscripts] j == AMINOACID_TO_NCBISTDAA['-']) { ^~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib/blast/blastn_score.cpp:944:41: warning: array subscript is of type 'char' [-Wchar-subscripts] x_index = AMINOACID_TO_NCBISTDAA['X']; ^~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib/blast/blastn_score.cpp:945:41: warning: array subscript is of type 'char' [-Wchar-subscripts] u_index = AMINOACID_TO_NCBISTDAA['U']; ^~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib/blast/blastn_score.cpp:946:41: warning: array subscript is of type 'char' [-Wchar-subscripts] o_index = AMINOACID_TO_NCBISTDAA['O']; ^~~~ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib/blast/blastn_score.cpp:947:41: warning: array subscript is of type 'char' [-Wchar-subscripts] c_index = AMINOACID_TO_NCBISTDAA['C']; ^~~~ 14 warnings generated. [ 93% 179/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/lib/blast/ncbi_std.cpp.o -MF CMakeFiles/diamond.dir/src/lib/blast/ncbi_std.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/blast/ncbi_std.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib/blast/ncbi_std.cpp [ 93% 180/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -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-2.1.9/src/util/tsv/table.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/util/tsv/table.cpp:6: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/util/tsv/../algo/transform_iterator.h:8:34: warning: 'result_of (const std::pair &)>' is deprecated [-Wdeprecated-declarations] using reference = typename std::result_of::type; ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/util/tsv/table.cpp:154:17: note: in instantiation of template class 'TransformIterator *>, Second>' requested here return shuffle(transform(v.begin(), Second()), transform(v.end(), Second())); ^ /usr/include/c++/v1/type_traits:3731:34: note: 'result_of (const std::pair &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:1030:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ 1 warning generated. [ 94% 181/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -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-2.1.9/src/util/tsv/file.cpp [ 94% 182/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/util/tsv/record.cpp.o -MF CMakeFiles/diamond.dir/src/util/tsv/record.cpp.o.d -o CMakeFiles/diamond.dir/src/util/tsv/record.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/util/tsv/record.cpp [ 95% 183/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/cluster/cascaded/helpers.cpp.o -MF CMakeFiles/diamond.dir/src/cluster/cascaded/helpers.cpp.o.d -o CMakeFiles/diamond.dir/src/cluster/cascaded/helpers.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/helpers.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/helpers.cpp:22: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/cascaded.h:23: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/../cluster.h:28: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/../../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/../../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 95% 184/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -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-2.1.9/src/cluster/cascaded/wrapper.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/wrapper.cpp:22: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/cascaded.h:23: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/../cluster.h:28: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/../../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/cluster/cascaded/../../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 96% 185/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT 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-2.1.9/src/output/daa/merge.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/daa/merge.cpp:24: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/daa/daa_write.h:24: In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/daa/../output.h:34: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/daa/../output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/output/daa/../output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. [ 96% 186/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/chaining/backtrace.cpp.o -MF CMakeFiles/diamond.dir/src/chaining/backtrace.cpp.o.d -o CMakeFiles/diamond.dir/src/chaining/backtrace.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/chaining/backtrace.cpp [ 97% 187/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/util/tsv/merge.cpp.o -MF CMakeFiles/diamond.dir/src/util/tsv/merge.cpp.o.d -o CMakeFiles/diamond.dir/src/util/tsv/merge.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/util/tsv/merge.cpp [ 97% 188/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/util/tsv/join.cpp.o -MF CMakeFiles/diamond.dir/src/util/tsv/join.cpp.o.d -o CMakeFiles/diamond.dir/src/util/tsv/join.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/util/tsv/join.cpp [ 98% 189/192] /ccache/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-2.1.9/src/lib -O2 -pipe -fstack-protector-strong -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 -Wno-pragma-clang-attribute -Wno-overloaded-virtual -Wno-missing-braces -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/dp/scalar/smith_waterman.cpp.o -MF CMakeFiles/diamond.dir/src/dp/scalar/smith_waterman.cpp.o.d -o CMakeFiles/diamond.dir/src/dp/scalar/smith_waterman.cpp.o -c /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/dp/scalar/smith_waterman.cpp In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/dp/scalar/smith_waterman.cpp:24: /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib/../output/output_format.h:148:24: warning: 'clone' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual OutputFormat* clone() const ^ /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.9/src/lib/../output/output_format.h:75:24: note: overridden virtual function is here virtual OutputFormat* clone() const = 0; ^ 1 warning generated. 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===> Staging for diamond-2.1.9 ===> 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 ====> 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=2024-04-05T14:30:50+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=92b051a290' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for diamond-2.1.9 ===> Building diamond-2.1.9 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for diamond-2.1.9 build of biology/diamond | diamond-2.1.9 ended at Fri Apr 5 15:48:53 BST 2024 build time: 00:18:04