=> Building biology/diamond Started : Thursday, 7 MAR 2019 at 18:12:34 UTC Platform: 5.5-DEVELOPMENT DragonFly v5.5.0.192.g15ae7f0-DEVELOPMENT #34: Tue Feb 19 09:07:07 PST 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.5-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.5-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/diamond XDG_CONFIG_HOME=/construction/biology/diamond HOME=/construction/biology/diamond TMPDIR="/tmp" PATH=/construction/biology/diamond/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/diamond XDG_CONFIG_HOME=/construction/biology/diamond HOME=/construction/biology/diamond TMPDIR="/tmp" PATH=/construction/biology/diamond/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -mtune=generic -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -mtune=generic -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/diamond/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- CMAKE_BUILD_TYPE="release" OSREL=5.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/diamond" EXAMPLESDIR="share/examples/diamond" DATADIR="share/diamond" WWWDIR="www/diamond" ETCDIR="etc/diamond" -------------------------------------------------- -- 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 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-BE USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.26.2 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500500 OSVERSION=9999999 OSREL=5.5 _OSRELEASE=5.5-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> diamond-0.9.24 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz Installing pkg-1.10.5_5... Extracting pkg-1.10.5_5: .......... done ===> diamond-0.9.24 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of diamond-0.9.24 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by diamond-0.9.24 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by diamond-0.9.24 for building => SHA256 Checksum OK for bbuchfink-diamond-v0.9.24_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by diamond-0.9.24 for building ===> Extracting for diamond-0.9.24 => SHA256 Checksum OK for bbuchfink-diamond-v0.9.24_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for diamond-0.9.24 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> diamond-0.9.24 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.13.4.txz Installing cmake-3.13.4... `-- Installing curl-7.64.0_1... | `-- Installing ca_root_nss-3.42.1... | `-- Extracting ca_root_nss-3.42.1: ........ done | `-- Installing krb5-1.17_1... | | `-- Installing gettext-runtime-0.19.8.1_2... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: .... done | | `-- Extracting gettext-runtime-0.19.8.1_2: .......... done | | `-- Installing libressl-2.8.3... | | `-- Extracting libressl-2.8.3: .......... done | | `-- Installing readline-7.0.5... | | `-- Installing ncurses-6.1.20190112... | | `-- Extracting ncurses-6.1.20190112: .......... done | | `-- Extracting readline-7.0.5: .......... done | `-- Extracting krb5-1.17_1: .......... done | `-- Installing libnghttp2-1.36.0... | `-- Extracting libnghttp2-1.36.0: .......... done `-- Extracting curl-7.64.0_1: .......... done `-- Installing expat-2.2.6_1... `-- Extracting expat-2.2.6_1: .......... done `-- Installing jsoncpp-1.8.1_5... `-- Extracting jsoncpp-1.8.1_5: .......... done `-- Installing libarchive-3.3.3,1... | `-- Installing liblz4-1.8.3,1... | `-- Extracting liblz4-1.8.3,1: .......... done | `-- Installing lzo2-2.10_1... | `-- Extracting lzo2-2.10_1: .......... done `-- Extracting libarchive-3.3.3,1: .......... done `-- Installing libuv-1.26.0... `-- Extracting libuv-1.26.0: .......... done `-- Installing rhash-1.3.5... `-- Extracting rhash-1.3.5: .......... done Extracting cmake-3.13.4: .......... done Message from ca_root_nss-3.42.1: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** ===> diamond-0.9.24 depends on file: /usr/local/bin/cmake - found ===> Returning to build of diamond-0.9.24 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for diamond-0.9.24 ===> Performing out-of-source build /bin/mkdir -p /construction/biology/diamond/.build -- The C compiler identification is GNU 8.1.0 -- The CXX compiler identification is GNU 8.1.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test COMPILER_SUPPORTS_MARCHNATIVE -- Performing Test COMPILER_SUPPORTS_MARCHNATIVE - Success -- Found ZLIB: /usr/lib/libz.so (found version "1.2.8") -- Looking for pthread.h -- Looking for pthread.h - found -- Found Threads: TRUE -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_CXX_FLAGS_DEBUG CMAKE_C_FLAGS_DEBUG CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS -- Build files have been written to: /construction/biology/diamond/.build -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for diamond-0.9.24 /usr/local/bin/cmake -S/construction/biology/diamond/diamond-0.9.24 -B/construction/biology/diamond/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/biology/diamond/.build/CMakeFiles /construction/biology/diamond/.build/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all --- CMakeFiles/diamond.dir/all --- /usr/bin/make -f CMakeFiles/diamond.dir/build.make CMakeFiles/diamond.dir/depend --- CMakeFiles/diamond.dir/depend --- cd /construction/biology/diamond/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/diamond/diamond-0.9.24 /construction/biology/diamond/diamond-0.9.24 /construction/biology/diamond/.build /construction/biology/diamond/.build /construction/biology/diamond/.build/CMakeFiles/diamond.dir/DependInfo.cmake Scanning dependencies of target diamond /usr/bin/make -f CMakeFiles/diamond.dir/build.make CMakeFiles/diamond.dir/build --- CMakeFiles/diamond.dir/src/run/main.cpp.o --- --- CMakeFiles/diamond.dir/src/basic/config.cpp.o --- --- CMakeFiles/diamond.dir/src/util/tinythread.cpp.o --- --- CMakeFiles/diamond.dir/src/basic/score_matrix.cpp.o --- --- CMakeFiles/diamond.dir/src/blast/blast_filter.cpp.o --- --- CMakeFiles/diamond.dir/src/basic/config.cpp.o --- [ 1%] Building CXX object CMakeFiles/diamond.dir/src/basic/config.cpp.o --- CMakeFiles/diamond.dir/src/blast/blast_filter.cpp.o --- [ 2%] Building CXX object CMakeFiles/diamond.dir/src/blast/blast_filter.cpp.o --- CMakeFiles/diamond.dir/src/basic/config.cpp.o --- /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized 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/usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/basic/score_matrix.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/basic/score_matrix.cpp --- CMakeFiles/diamond.dir/src/run/main.cpp.o --- /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/run/main.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/run/main.cpp --- CMakeFiles/diamond.dir/src/util/tinythread.cpp.o --- [ 5%] Building CXX object CMakeFiles/diamond.dir/src/util/tinythread.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/util/tinythread.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/util/tinythread.cpp --- CMakeFiles/diamond.dir/src/blast/blast_seg.cpp.o --- [ 6%] Building CXX object CMakeFiles/diamond.dir/src/blast/blast_seg.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/blast/blast_seg.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/blast/blast_seg.cpp --- CMakeFiles/diamond.dir/src/blast/sm_blosum45.c.o --- [ 7%] Building C object CMakeFiles/diamond.dir/src/blast/sm_blosum45.c.o /usr/bin/cc -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -pipe -mtune=generic -O2 -fno-strict-aliasing -o CMakeFiles/diamond.dir/src/blast/sm_blosum45.c.o -c /construction/biology/diamond/diamond-0.9.24/src/blast/sm_blosum45.c --- CMakeFiles/diamond.dir/src/blast/sm_blosum50.c.o --- [ 8%] Building C object CMakeFiles/diamond.dir/src/blast/sm_blosum50.c.o /usr/bin/cc -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -pipe -mtune=generic -O2 -fno-strict-aliasing -o CMakeFiles/diamond.dir/src/blast/sm_blosum50.c.o -c /construction/biology/diamond/diamond-0.9.24/src/blast/sm_blosum50.c --- CMakeFiles/diamond.dir/src/blast/sm_blosum62.c.o --- [ 10%] Building C object CMakeFiles/diamond.dir/src/blast/sm_blosum62.c.o /usr/bin/cc -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -pipe -mtune=generic 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CMakeFiles/diamond.dir/src/blast/sm_pam30.c.o --- [ 13%] Building C object CMakeFiles/diamond.dir/src/blast/sm_pam30.c.o /usr/bin/cc -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -pipe -mtune=generic -O2 -fno-strict-aliasing -o CMakeFiles/diamond.dir/src/blast/sm_pam30.c.o -c /construction/biology/diamond/diamond-0.9.24/src/blast/sm_pam30.c --- CMakeFiles/diamond.dir/src/blast/sm_pam70.c.o --- [ 14%] Building C object CMakeFiles/diamond.dir/src/blast/sm_pam70.c.o /usr/bin/cc -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -pipe -mtune=generic -O2 -fno-strict-aliasing -o CMakeFiles/diamond.dir/src/blast/sm_pam70.c.o -c /construction/biology/diamond/diamond-0.9.24/src/blast/sm_pam70.c --- CMakeFiles/diamond.dir/src/blast/sm_pam250.c.o --- --- CMakeFiles/diamond.dir/src/data/queries.cpp.o --- --- CMakeFiles/diamond.dir/src/blast/sm_pam250.c.o --- [ 15%] Building C object CMakeFiles/diamond.dir/src/blast/sm_pam250.c.o /usr/bin/cc -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -pipe -mtune=generic -O2 -fno-strict-aliasing -o CMakeFiles/diamond.dir/src/blast/sm_pam250.c.o -c /construction/biology/diamond/diamond-0.9.24/src/blast/sm_pam250.c --- CMakeFiles/diamond.dir/src/data/queries.cpp.o --- [ 16%] Building CXX object CMakeFiles/diamond.dir/src/data/queries.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/data/queries.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/data/queries.cpp --- CMakeFiles/diamond.dir/src/data/reference.cpp.o --- [ 17%] Building CXX object CMakeFiles/diamond.dir/src/data/reference.cpp.o /usr/bin/c++ 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-I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/extra/model_sim.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/extra/model_sim.cpp --- CMakeFiles/diamond.dir/src/run/double_indexed.cpp.o --- [ 45%] Building CXX object CMakeFiles/diamond.dir/src/run/double_indexed.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/run/double_indexed.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/run/double_indexed.cpp --- CMakeFiles/diamond.dir/src/search/collision.cpp.o --- [ 46%] Building CXX object CMakeFiles/diamond.dir/src/search/collision.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/search/collision.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/search/collision.cpp --- CMakeFiles/diamond.dir/src/output/sam_format.cpp.o --- [ 47%] Building CXX object CMakeFiles/diamond.dir/src/output/sam_format.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/output/sam_format.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/output/sam_format.cpp --- CMakeFiles/diamond.dir/src/align/align.cpp.o --- [ 48%] Building CXX object CMakeFiles/diamond.dir/src/align/align.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/align/align.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/align/align.cpp --- CMakeFiles/diamond.dir/src/search/setup.cpp.o --- [ 50%] Building CXX object CMakeFiles/diamond.dir/src/search/setup.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/search/setup.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/search/setup.cpp --- CMakeFiles/diamond.dir/src/run/double_indexed.cpp.o --- In file included from /construction/biology/diamond/diamond-0.9.24/src/run/../data/reference.h:28, from /construction/biology/diamond/diamond-0.9.24/src/run/double_indexed.cpp:22: /construction/biology/diamond/diamond-0.9.24/src/run/../data/../data/seed_histogram.h: In instantiation of 'Partitioned_histogram::Partitioned_histogram(const Sequence_set&, bool, const _filter*) [with _filter = Seed_set]': /construction/biology/diamond/diamond-0.9.24/src/run/double_indexed.cpp:143:71: required from here /construction/biology/diamond/diamond-0.9.24/src/run/../data/../data/seed_histogram.h:96:10: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Array'; use assignment or value-initialization instead [-Wclass-memaccess] memset(data_[s].data(), 0, (p_.size() - 1)*sizeof(unsigned)*Const::seedp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /construction/biology/diamond/diamond-0.9.24/src/run/../data/../util/io/../text_buffer.h:28, from /construction/biology/diamond/diamond-0.9.24/src/run/../data/../util/io/output_file.h:27, from /construction/biology/diamond/diamond-0.9.24/src/run/../data/../util/io/input_file.h:25, from /construction/biology/diamond/diamond-0.9.24/src/run/../data/reference.h:27, from /construction/biology/diamond/diamond-0.9.24/src/run/double_indexed.cpp:22: /construction/biology/diamond/diamond-0.9.24/src/run/../data/../util/io/../util.h:211:8: note: 'struct Array' declared here struct Array ^~~~~ In file included from /construction/biology/diamond/diamond-0.9.24/src/run/../data/reference.h:28, from /construction/biology/diamond/diamond-0.9.24/src/run/double_indexed.cpp:22: /construction/biology/diamond/diamond-0.9.24/src/run/../data/../data/seed_histogram.h: In instantiation of 'Partitioned_histogram::Partitioned_histogram(const Sequence_set&, bool, const _filter*) [with _filter = Hashed_seed_set]': /construction/biology/diamond/diamond-0.9.24/src/run/double_indexed.cpp:145:77: required from here /construction/biology/diamond/diamond-0.9.24/src/run/../data/../data/seed_histogram.h:96:10: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Array'; use assignment or value-initialization instead [-Wclass-memaccess] memset(data_[s].data(), 0, (p_.size() - 1)*sizeof(unsigned)*Const::seedp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /construction/biology/diamond/diamond-0.9.24/src/run/../data/../util/io/../text_buffer.h:28, from /construction/biology/diamond/diamond-0.9.24/src/run/../data/../util/io/output_file.h:27, from /construction/biology/diamond/diamond-0.9.24/src/run/../data/../util/io/input_file.h:25, from /construction/biology/diamond/diamond-0.9.24/src/run/../data/reference.h:27, from /construction/biology/diamond/diamond-0.9.24/src/run/double_indexed.cpp:22: /construction/biology/diamond/diamond-0.9.24/src/run/../data/../util/io/../util.h:211:8: note: 'struct Array' declared here struct Array ^~~~~ In file included from /construction/biology/diamond/diamond-0.9.24/src/run/../data/reference.h:28, from /construction/biology/diamond/diamond-0.9.24/src/run/double_indexed.cpp:22: /construction/biology/diamond/diamond-0.9.24/src/run/../data/../data/seed_histogram.h: In instantiation of 'Partitioned_histogram::Partitioned_histogram(const Sequence_set&, bool, const _filter*) [with _filter = No_filter]': /construction/biology/diamond/diamond-0.9.24/src/run/double_indexed.cpp:147:70: required from here /construction/biology/diamond/diamond-0.9.24/src/run/../data/../data/seed_histogram.h:96:10: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Array'; use assignment or value-initialization instead [-Wclass-memaccess] memset(data_[s].data(), 0, (p_.size() - 1)*sizeof(unsigned)*Const::seedp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /construction/biology/diamond/diamond-0.9.24/src/run/../data/../util/io/../text_buffer.h:28, from /construction/biology/diamond/diamond-0.9.24/src/run/../data/../util/io/output_file.h:27, from /construction/biology/diamond/diamond-0.9.24/src/run/../data/../util/io/input_file.h:25, from /construction/biology/diamond/diamond-0.9.24/src/run/../data/reference.h:27, from /construction/biology/diamond/diamond-0.9.24/src/run/double_indexed.cpp:22: /construction/biology/diamond/diamond-0.9.24/src/run/../data/../util/io/../util.h:211:8: note: 'struct Array' declared here struct Array ^~~~~ --- CMakeFiles/diamond.dir/src/extra/opt.cpp.o --- [ 51%] Building CXX object CMakeFiles/diamond.dir/src/extra/opt.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/extra/opt.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/extra/opt.cpp --- CMakeFiles/diamond.dir/src/dp/diag_scores.cpp.o --- [ 52%] Building CXX object CMakeFiles/diamond.dir/src/dp/diag_scores.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/dp/diag_scores.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/dp/diag_scores.cpp --- CMakeFiles/diamond.dir/src/data/taxonomy.cpp.o --- [ 53%] Building CXX object CMakeFiles/diamond.dir/src/data/taxonomy.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/data/taxonomy.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/data/taxonomy.cpp --- CMakeFiles/diamond.dir/src/lib/tantan/tantan.cc.o --- [ 54%] Building CXX object CMakeFiles/diamond.dir/src/lib/tantan/tantan.cc.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/lib/tantan/tantan.cc.o -c /construction/biology/diamond/diamond-0.9.24/src/lib/tantan/tantan.cc --- CMakeFiles/diamond.dir/src/basic/masking.cpp.o --- [ 55%] Building CXX object CMakeFiles/diamond.dir/src/basic/masking.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/basic/masking.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/basic/masking.cpp --- CMakeFiles/diamond.dir/src/dp/swipe/swipe.cpp.o --- [ 56%] Building CXX object CMakeFiles/diamond.dir/src/dp/swipe/swipe.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/dp/swipe/swipe.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/swipe.cpp --- CMakeFiles/diamond.dir/src/dp/banded_sw.cpp.o --- [ 57%] Building CXX object CMakeFiles/diamond.dir/src/dp/banded_sw.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/dp/banded_sw.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/dp/banded_sw.cpp --- CMakeFiles/diamond.dir/src/data/sorted_list.cpp.o --- [ 58%] Building CXX object CMakeFiles/diamond.dir/src/data/sorted_list.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/data/sorted_list.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/data/sorted_list.cpp --- CMakeFiles/diamond.dir/src/data/seed_set.cpp.o --- [ 60%] Building CXX object CMakeFiles/diamond.dir/src/data/seed_set.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/data/seed_set.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/data/seed_set.cpp --- CMakeFiles/diamond.dir/src/data/taxonomy.cpp.o --- In file included from /construction/biology/diamond/diamond-0.9.24/src/data/taxonomy.cpp:21: In constructor 'Taxonomy::Accession::Accession(const string&)', inlined from 'void Taxonomy::get_taxids(const char*, std::set&) const' at /construction/biology/diamond/diamond-0.9.24/src/data/taxonomy.cpp:120:37: /construction/biology/diamond/diamond-0.9.24/src/data/taxonomy.h:59:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 14 equals destination size [-Wstringop-truncation] strncpy(this->s, t.c_str(), max_accesion_len); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --- CMakeFiles/diamond.dir/src/util/simd.cpp.o --- [ 61%] Building CXX object CMakeFiles/diamond.dir/src/util/simd.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/util/simd.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/util/simd.cpp --- CMakeFiles/diamond.dir/src/output/taxon_format.cpp.o --- [ 62%] Building CXX object CMakeFiles/diamond.dir/src/output/taxon_format.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/output/taxon_format.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/output/taxon_format.cpp --- CMakeFiles/diamond.dir/src/output/view.cpp.o --- [ 63%] Building CXX object CMakeFiles/diamond.dir/src/output/view.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/output/view.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/output/view.cpp --- CMakeFiles/diamond.dir/src/dp/swipe/swipe.cpp.o --- In file included from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/swipe.cpp:22: /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/swipe_matrix.h: In instantiation of 'SwipeMatrix<_sv>::SwipeMatrix(int) [with _sv = score_vector]': /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/swipe.cpp:44:19: required from 'void swipe(const sequence&, std::vector::const_iterator, std::vector::const_iterator, std::vector::iterator) [with _sv = score_vector; std::vector::const_iterator = __gnu_cxx::__normal_iterator >; std::vector::iterator = __gnu_cxx::__normal_iterator >]' /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/swipe.cpp:100:70: required from here /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/swipe_matrix.h:71:9: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct score_vector'; use assignment or value-initialization instead [-Wclass-memaccess] memset(hgap_.data(), 0, rows * sizeof(_sv)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/swipe.cpp:20: /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/../score_vector.h:49:8: note: 'struct score_vector' declared here struct score_vector ^~~~~~~~~~~~~~~~~~~~~ In file included from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/swipe.cpp:22: /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/swipe_matrix.h:72:9: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct score_vector'; use assignment or value-initialization instead [-Wclass-memaccess] memset(score_.data(), 0, (rows + 1) * sizeof(_sv)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/swipe.cpp:20: /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/../score_vector.h:49:8: note: 'struct score_vector' declared here struct score_vector ^~~~~~~~~~~~~~~~~~~~~ --- CMakeFiles/diamond.dir/src/output/output_sink.cpp.o --- [ 64%] Building CXX object CMakeFiles/diamond.dir/src/output/output_sink.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/output/output_sink.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/output/output_sink.cpp --- CMakeFiles/diamond.dir/src/output/target_culling.cpp.o --- [ 65%] Building CXX object CMakeFiles/diamond.dir/src/output/target_culling.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/output/target_culling.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/output/target_culling.cpp --- CMakeFiles/diamond.dir/src/align/greedy_pipeline.cpp.o --- [ 66%] Building CXX object CMakeFiles/diamond.dir/src/align/greedy_pipeline.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/align/greedy_pipeline.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/align/greedy_pipeline.cpp --- CMakeFiles/diamond.dir/src/align/swipe_pipeline.cpp.o --- [ 67%] Building CXX object CMakeFiles/diamond.dir/src/align/swipe_pipeline.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/align/swipe_pipeline.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/align/swipe_pipeline.cpp --- CMakeFiles/diamond.dir/src/dp/swipe/banded_3frame_swipe.cpp.o --- [ 68%] Building CXX object CMakeFiles/diamond.dir/src/dp/swipe/banded_3frame_swipe.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/dp/swipe/banded_3frame_swipe.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/banded_3frame_swipe.cpp --- CMakeFiles/diamond.dir/src/dp/swipe/banded_swipe.cpp.o --- [ 70%] Building CXX object CMakeFiles/diamond.dir/src/dp/swipe/banded_swipe.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/dp/swipe/banded_swipe.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/banded_swipe.cpp --- CMakeFiles/diamond.dir/src/align/banded_swipe_pipeline.cpp.o --- [ 71%] Building CXX object CMakeFiles/diamond.dir/src/align/banded_swipe_pipeline.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/align/banded_swipe_pipeline.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/align/banded_swipe_pipeline.cpp --- CMakeFiles/diamond.dir/src/data/ref_dictionary.cpp.o --- [ 72%] Building CXX object CMakeFiles/diamond.dir/src/data/ref_dictionary.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/data/ref_dictionary.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/data/ref_dictionary.cpp --- CMakeFiles/diamond.dir/src/util/io/compressed_stream.cpp.o --- [ 73%] Building CXX object CMakeFiles/diamond.dir/src/util/io/compressed_stream.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/util/io/compressed_stream.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/util/io/compressed_stream.cpp --- CMakeFiles/diamond.dir/src/util/io/deserializer.cpp.o --- [ 74%] Building CXX object CMakeFiles/diamond.dir/src/util/io/deserializer.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/util/io/deserializer.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/util/io/deserializer.cpp --- CMakeFiles/diamond.dir/src/util/io/file_sink.cpp.o --- [ 75%] Building CXX object CMakeFiles/diamond.dir/src/util/io/file_sink.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/util/io/file_sink.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/util/io/file_sink.cpp --- CMakeFiles/diamond.dir/src/util/io/file_source.cpp.o --- [ 76%] Building CXX object CMakeFiles/diamond.dir/src/util/io/file_source.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/util/io/file_source.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/util/io/file_source.cpp --- CMakeFiles/diamond.dir/src/dp/swipe/banded_3frame_swipe.cpp.o --- In file included from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/../../basic/../basic/value.h:28, from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/../../basic/sequence.h:24, from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/../../basic/match.h:24, from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/../dp.h:27, from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/banded_3frame_swipe.cpp:20: In member function 'void Static_vector<_t, _n>::erase(int) [with _t = int; int _n = 8]', inlined from 'void banded_3frame_swipe(const TranslatedSequence&, Strand, std::vector::iterator, std::vector::iterator, DpStat&, bool) [with _sv = score_vector; _traceback = Traceback]' at /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/banded_3frame_swipe.cpp:207:5: /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/../../basic/../basic/../util/util.h:262:10: warning: 'void* memmove(void*, const void*, size_t)' offset [-4, -8] is out of the bounds [0, 120] of object 'targets' with type 'TargetIterator<8>' [-Warray-bounds] memmove(&data[i], &data[i + 1], (--n - i)*sizeof(_t)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/banded_3frame_swipe.cpp: In function 'void banded_3frame_swipe(const TranslatedSequence&, Strand, std::vector::iterator, std::vector::iterator, DpStat&, bool) [with _sv = score_vector; _traceback = Traceback]': /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/banded_3frame_swipe.cpp:148:45: note: 'targets' declared here TargetIterator::CHANNELS> targets(subject_begin, subject_end, i1, qlen); ^~~~~~~ --- CMakeFiles/diamond.dir/src/util/io/input_file.cpp.o --- [ 77%] Building CXX object CMakeFiles/diamond.dir/src/util/io/input_file.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/util/io/input_file.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/util/io/input_file.cpp --- CMakeFiles/diamond.dir/src/dp/swipe/banded_3frame_swipe.cpp.o --- In file included from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/../../basic/../basic/value.h:28, from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/../../basic/sequence.h:24, from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/../../basic/match.h:24, from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/../dp.h:27, from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/banded_3frame_swipe.cpp:20: In member function 'void Static_vector<_t, _n>::erase(int) [with _t = int; int _n = 8]', inlined from 'void banded_3frame_swipe(const TranslatedSequence&, Strand, std::vector::iterator, std::vector::iterator, DpStat&, bool) [with _sv = score_vector; _traceback = ScoreOnly]' at /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/banded_3frame_swipe.cpp:207:5: /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/../../basic/../basic/../util/util.h:262:10: warning: 'void* memmove(void*, const void*, size_t)' offset [-4, -8] is out of the bounds [0, 120] of object 'targets' with type 'TargetIterator<8>' [-Warray-bounds] memmove(&data[i], &data[i + 1], (--n - i)*sizeof(_t)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/banded_3frame_swipe.cpp: In function 'void banded_3frame_swipe(const TranslatedSequence&, Strand, std::vector::iterator, std::vector::iterator, DpStat&, bool) [with _sv = score_vector; _traceback = ScoreOnly]': /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/banded_3frame_swipe.cpp:148:45: note: 'targets' declared here TargetIterator::CHANNELS> targets(subject_begin, subject_end, i1, qlen); ^~~~~~~ --- CMakeFiles/diamond.dir/src/util/io/input_stream_buffer.cpp.o --- [ 78%] Building CXX object CMakeFiles/diamond.dir/src/util/io/input_stream_buffer.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/util/io/input_stream_buffer.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/util/io/input_stream_buffer.cpp --- CMakeFiles/diamond.dir/src/dp/swipe/banded_3frame_swipe.cpp.o --- In file included from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/../../basic/../basic/value.h:28, from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/../../basic/sequence.h:24, from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/../../basic/match.h:24, from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/../dp.h:27, from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/banded_3frame_swipe.cpp:20: In member function 'void Static_vector<_t, _n>::erase(int) [with _t = int; int _n = 1]', inlined from 'void banded_3frame_swipe(const TranslatedSequence&, Strand, std::vector::iterator, std::vector::iterator, DpStat&, bool) [with _sv = int; _traceback = Traceback]' at /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/banded_3frame_swipe.cpp:207:5: /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/../../basic/../basic/../util/util.h:262:10: warning: 'void* memmove(void*, const void*, size_t)' offset [-4, -8] is out of the bounds [0, 40] of object 'targets' with type 'TargetIterator<1>' [-Warray-bounds] memmove(&data[i], &data[i + 1], (--n - i)*sizeof(_t)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/banded_3frame_swipe.cpp: In function 'void banded_3frame_swipe(const TranslatedSequence&, Strand, std::vector::iterator, std::vector::iterator, DpStat&, bool) [with _sv = int; _traceback = Traceback]': /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/banded_3frame_swipe.cpp:148:45: note: 'targets' declared here TargetIterator::CHANNELS> targets(subject_begin, subject_end, i1, qlen); ^~~~~~~ --- CMakeFiles/diamond.dir/src/util/io/output_file.cpp.o --- [ 80%] Building CXX object CMakeFiles/diamond.dir/src/util/io/output_file.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/util/io/output_file.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/util/io/output_file.cpp --- CMakeFiles/diamond.dir/src/dp/swipe/banded_3frame_swipe.cpp.o --- In file included from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/../../basic/../basic/value.h:28, from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/../../basic/sequence.h:24, from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/../../basic/match.h:24, from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/../dp.h:27, from /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/banded_3frame_swipe.cpp:20: In member function 'void Static_vector<_t, _n>::erase(int) [with _t = int; int _n = 1]', inlined from 'void banded_3frame_swipe(const TranslatedSequence&, Strand, std::vector::iterator, std::vector::iterator, DpStat&, bool) [with _sv = int; _traceback = ScoreOnly]' at /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/banded_3frame_swipe.cpp:207:5: /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/../../basic/../basic/../util/util.h:262:10: warning: 'void* memmove(void*, const void*, size_t)' offset [-4, -8] is out of the bounds [0, 40] of object 'targets' with type 'TargetIterator<1>' [-Warray-bounds] memmove(&data[i], &data[i + 1], (--n - i)*sizeof(_t)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/banded_3frame_swipe.cpp: In function 'void banded_3frame_swipe(const TranslatedSequence&, Strand, std::vector::iterator, std::vector::iterator, DpStat&, bool) [with _sv = int; _traceback = ScoreOnly]': /construction/biology/diamond/diamond-0.9.24/src/dp/swipe/banded_3frame_swipe.cpp:148:45: note: 'targets' declared here TargetIterator::CHANNELS> targets(subject_begin, subject_end, i1, qlen); ^~~~~~~ --- CMakeFiles/diamond.dir/src/util/io/output_stream_buffer.cpp.o --- [ 81%] Building CXX object CMakeFiles/diamond.dir/src/util/io/output_stream_buffer.cpp.o /usr/bin/c++ -I/construction/biology/diamond/diamond-0.9.24/src -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -march=native -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o 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-pipe -mtune=generic -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/util/system/system.cpp.o -c /construction/biology/diamond/diamond-0.9.24/src/util/system/system.cpp --- CMakeFiles/diamond.dir/src/search/stage0.cpp.o --- In file included from /construction/biology/diamond/diamond-0.9.24/src/search/../util/algo/hash_join.h:26, from /construction/biology/diamond/diamond-0.9.24/src/search/stage0.cpp:20: /construction/biology/diamond/diamond-0.9.24/src/search/../util/algo/../data_structures/hash_table.h: In instantiation of 'HashTable<_K, _V, _HashFunction>::HashTable(size_t, const _HashFunction&) [with _K = unsigned int; _V = RelPtr; _HashFunction = ExtractBits; size_t = long unsigned int]': /construction/biology/diamond/diamond-0.9.24/src/search/../util/algo/hash_join.h:52:8: required from 'void hash_table_join(const Relation<_t>&, const Relation<_t>&, unsigned int, JoinResult<_t>&) [with _t = SeedArray::Entry]' /construction/biology/diamond/diamond-0.9.24/src/search/../util/algo/hash_join.h:175:19: required from 'void hash_join(const Relation<_t>&, const Relation<_t>&, JoinResult<_t>&, MemoryPool&, unsigned int, unsigned int) [with _t = SeedArray::Entry]' /construction/biology/diamond/diamond-0.9.24/src/search/stage0.cpp:39:6: required from here /construction/biology/diamond/diamond-0.9.24/src/search/../util/algo/../data_structures/hash_table.h:42:9: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct HashTable::Entry'; use assignment or value-initialization instead [-Wclass-memaccess] memset(table, 0, size_ * sizeof(Entry)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /construction/biology/diamond/diamond-0.9.24/src/search/../util/algo/../data_structures/hash_table.h:28:9: note: 'struct HashTable::Entry' declared here struct Entry : public _V ^~~~~ --- CMakeFiles/diamond.dir/src/run/cluster.cpp.o --- [ 94%] Building CXX object 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