=>> Building biology/megahit build started at Thu Apr 4 20:10:04 BST 2024 port directory: /usr/ports/biology/megahit package name: megahit-1.2.9_1 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 536 Mar 8 2023 /usr/ports/biology/megahit/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: c014f9c79a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 12 ---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 LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/12/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/megahit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/megahit/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/megahit/work/.cache HOME=/wrkdirs/usr/ports/biology/megahit/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/megahit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/megahit/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCACHE_DIR="/root/.ccache" --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/megahit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/megahit/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/megahit/work/.cache HOME=/wrkdirs/usr/ports/biology/megahit/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/megahit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/megahit/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/megahit/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -pthread -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" PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/megahit" EXAMPLESDIR="share/examples/megahit" DATADIR="share/megahit" WWWDIR="www/megahit" ETCDIR="etc/megahit" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/megahit DOCSDIR=/usr/local/share/doc/megahit EXAMPLESDIR=/usr/local/share/examples/megahit WWWDIR=/usr/local/www/megahit ETCDIR=/usr/local/etc/megahit --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 ===> megahit-1.2.9_1 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 ===> megahit-1.2.9_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of megahit-1.2.9_1 =========================================================================== =================================================== ===== 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 megahit-1.2.9_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by megahit-1.2.9_1 for building => SHA256 Checksum OK for voutcn-megahit-v1.2.9_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 megahit-1.2.9_1 for building ===> Extracting for megahit-1.2.9_1 => SHA256 Checksum OK for voutcn-megahit-v1.2.9_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 megahit-1.2.9_1 ===> Applying FreeBSD patches for megahit-1.2.9_1 from /usr/ports/biology/megahit/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> megahit-1.2.9_1 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 ===> megahit-1.2.9_1 depends on file: /usr/local/bin/cmake - found ===> Returning to build of megahit-1.2.9_1 ===> megahit-1.2.9_1 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 ===> megahit-1.2.9_1 depends on executable: ninja - found ===> Returning to build of megahit-1.2.9_1 ===> megahit-1.2.9_1 depends on file: /usr/local/bin/python3.9 - found =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for megahit-1.2.9_1 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/megahit/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 -- Found ZLIB: /usr/lib/libz.so (found version "1.2.13") -- Found OpenMP_C: -fopenmp=libomp (found version "5.0") -- Found OpenMP_CXX: -fopenmp=libomp (found version "5.0") -- Found OpenMP: TRUE (found version "5.0") -- Build type: Release: -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -- Configuring done (1.7s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: BOOST_PYTHON_SUFFIX CMAKE_COLOR_MAKEFILE CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS FETCHCONTENT_FULLY_DISCONNECTED Python3_EXECUTABLE Python_ADDITIONAL_VERSIONS Python_EXECUTABLE THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/biology/megahit/work/.build =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for megahit-1.2.9_1 [ 0% 1/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/main.cpp.o -MF CMakeFiles/megahit_core.dir/src/main.cpp.o.d -o CMakeFiles/megahit_core.dir/src/main.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main.cpp [ 1% 2/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/main_assemble.cpp.o -MF CMakeFiles/megahit_core.dir/src/main_assemble.cpp.o.d -o CMakeFiles/megahit_core.dir/src/main_assemble.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_assemble.cpp [ 2% 3/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/main_buildlib.cpp.o -MF CMakeFiles/megahit_core.dir/src/main_buildlib.cpp.o.d -o CMakeFiles/megahit_core.dir/src/main_buildlib.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_buildlib.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_buildlib.cpp:1: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.h:31: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 1 warning generated. [ 3% 4/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/main_iterate.cpp.o -MF CMakeFiles/megahit_core.dir/src/main_iterate.cpp.o.d -o CMakeFiles/megahit_core.dir/src/main_iterate.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_iterate.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_iterate.cpp:38: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/async_sequence_reader.h:10: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 1 warning generated. [ 4% 5/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/main_local_assemble.cpp.o -MF CMakeFiles/megahit_core.dir/src/main_local_assemble.cpp.o.d -o CMakeFiles/megahit_core.dir/src/main_local_assemble.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_local_assemble.cpp [ 5% 6/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/main_sdbg_build.cpp.o -MF CMakeFiles/megahit_core.dir/src/main_sdbg_build.cpp.o.d -o CMakeFiles/megahit_core.dir/src/main_sdbg_build.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_sdbg_build.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_sdbg_build.cpp:29: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmer_counter.h:53:18: warning: class with destructor marked 'final' cannot be inherited from [-Wfinal-dtor-non-final-class] ~KmerCounter() final = default; ^ /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmer_counter.h:46:7: note: mark 'KmerCounter' as 'final' to silence this warning class KmerCounter : public BaseSequenceSortingEngine { ^ In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_sdbg_build.cpp:30: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/read_to_sdbg.h:33: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.h:31: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 2 warnings generated. [ 6% 7/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/utils/options_description.cpp.o -MF CMakeFiles/megahit_core.dir/src/utils/options_description.cpp.o.d -o CMakeFiles/megahit_core.dir/src/utils/options_description.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/utils/options_description.cpp [ 7% 8/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/assembly/bubble_remover.cpp.o -MF CMakeFiles/megahit_core.dir/src/assembly/bubble_remover.cpp.o.d -o CMakeFiles/megahit_core.dir/src/assembly/bubble_remover.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/assembly/bubble_remover.cpp [ 8% 9/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/assembly/contig_output.cpp.o -MF CMakeFiles/megahit_core.dir/src/assembly/contig_output.cpp.o.d -o CMakeFiles/megahit_core.dir/src/assembly/contig_output.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/assembly/contig_output.cpp [ 9% 10/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/assembly/low_depth_remover.cpp.o -MF CMakeFiles/megahit_core.dir/src/assembly/low_depth_remover.cpp.o.d -o CMakeFiles/megahit_core.dir/src/assembly/low_depth_remover.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/assembly/low_depth_remover.cpp [ 10% 11/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/assembly/sdbg_pruning.cpp.o -MF CMakeFiles/megahit_core.dir/src/assembly/sdbg_pruning.cpp.o.d -o CMakeFiles/megahit_core.dir/src/assembly/sdbg_pruning.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/assembly/sdbg_pruning.cpp [ 10% 12/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/assembly/tip_remover.cpp.o -MF CMakeFiles/megahit_core.dir/src/assembly/tip_remover.cpp.o.d -o CMakeFiles/megahit_core.dir/src/assembly/tip_remover.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/assembly/tip_remover.cpp [ 11% 13/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/assembly/unitig_graph.cpp.o -MF CMakeFiles/megahit_core.dir/src/assembly/unitig_graph.cpp.o.d -o CMakeFiles/megahit_core.dir/src/assembly/unitig_graph.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/assembly/unitig_graph.cpp [ 12% 14/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/assembly/weak_link_remover.cpp.o -MF CMakeFiles/megahit_core.dir/src/assembly/weak_link_remover.cpp.o.d -o CMakeFiles/megahit_core.dir/src/assembly/weak_link_remover.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/assembly/weak_link_remover.cpp [ 13% 15/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/idba/contig_graph.cpp.o -MF CMakeFiles/megahit_core.dir/src/idba/contig_graph.cpp.o.d -o CMakeFiles/megahit_core.dir/src/idba/contig_graph.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/idba/contig_graph.cpp [ 14% 16/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/idba/contig_graph_branch_group.cpp.o -MF CMakeFiles/megahit_core.dir/src/idba/contig_graph_branch_group.cpp.o.d -o CMakeFiles/megahit_core.dir/src/idba/contig_graph_branch_group.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/idba/contig_graph_branch_group.cpp [ 15% 17/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/idba/hash_graph.cpp.o -MF CMakeFiles/megahit_core.dir/src/idba/hash_graph.cpp.o.d -o CMakeFiles/megahit_core.dir/src/idba/hash_graph.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/idba/hash_graph.cpp [ 16% 18/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/idba/sequence.cpp.o -MF CMakeFiles/megahit_core.dir/src/idba/sequence.cpp.o.d -o CMakeFiles/megahit_core.dir/src/idba/sequence.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/idba/sequence.cpp [ 17% 19/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/sdbg/sdbg_meta.cpp.o -MF CMakeFiles/megahit_core.dir/src/sdbg/sdbg_meta.cpp.o.d -o CMakeFiles/megahit_core.dir/src/sdbg/sdbg_meta.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sdbg/sdbg_meta.cpp [ 18% 20/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/sdbg/sdbg_raw_content.cpp.o -MF CMakeFiles/megahit_core.dir/src/sdbg/sdbg_raw_content.cpp.o.d -o CMakeFiles/megahit_core.dir/src/sdbg/sdbg_raw_content.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sdbg/sdbg_raw_content.cpp /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sdbg/sdbg_raw_content.cpp:39:10: warning: variable 'file_offset' set but not used [-Wunused-but-set-variable] size_t file_offset = 0; ^ 1 warning generated. [ 19% 21/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/sdbg/sdbg_writer.cpp.o -MF CMakeFiles/megahit_core.dir/src/sdbg/sdbg_writer.cpp.o.d -o CMakeFiles/megahit_core.dir/src/sdbg/sdbg_writer.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sdbg/sdbg_writer.cpp [ 20% 22/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/localasm/hash_mapper.cpp.o -MF CMakeFiles/megahit_core.dir/src/localasm/hash_mapper.cpp.o.d -o CMakeFiles/megahit_core.dir/src/localasm/hash_mapper.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/localasm/hash_mapper.cpp [ 20% 23/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/localasm/local_assemble.cpp.o -MF CMakeFiles/megahit_core.dir/src/localasm/local_assemble.cpp.o.d -o CMakeFiles/megahit_core.dir/src/localasm/local_assemble.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/localasm/local_assemble.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/localasm/local_assemble.cpp:19: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.h:31: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 1 warning generated. [ 21% 24/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/sequence/io/fastx_reader.cpp.o -MF CMakeFiles/megahit_core.dir/src/sequence/io/fastx_reader.cpp.o.d -o CMakeFiles/megahit_core.dir/src/sequence/io/fastx_reader.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/fastx_reader.cpp [ 22% 25/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/sequence/io/paired_fastx_reader.cpp.o -MF CMakeFiles/megahit_core.dir/src/sequence/io/paired_fastx_reader.cpp.o.d -o CMakeFiles/megahit_core.dir/src/sequence/io/paired_fastx_reader.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/paired_fastx_reader.cpp [ 23% 26/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/sequence/io/sequence_lib.cpp.o -MF CMakeFiles/megahit_core.dir/src/sequence/io/sequence_lib.cpp.o.d -o CMakeFiles/megahit_core.dir/src/sequence/io/sequence_lib.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.cpp:5: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.h:31: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 1 warning generated. [ 24% 27/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/sorting/base_engine.cpp.o -MF CMakeFiles/megahit_core.dir/src/sorting/base_engine.cpp.o.d -o CMakeFiles/megahit_core.dir/src/sorting/base_engine.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/base_engine.cpp [ 25% 28/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/sorting/kmer_counter.cpp.o -MF CMakeFiles/megahit_core.dir/src/sorting/kmer_counter.cpp.o.d -o CMakeFiles/megahit_core.dir/src/sorting/kmer_counter.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmer_counter.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmer_counter.cpp:1: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmer_counter.h:53:18: warning: class with destructor marked 'final' cannot be inherited from [-Wfinal-dtor-non-final-class] ~KmerCounter() final = default; ^ /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmer_counter.h:46:7: note: mark 'KmerCounter' as 'final' to silence this warning class KmerCounter : public BaseSequenceSortingEngine { ^ In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmer_counter.cpp:6: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.h:31: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 2 warnings generated. [ 26% 29/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/sorting/kmsort_selector.cpp.o -MF CMakeFiles/megahit_core.dir/src/sorting/kmsort_selector.cpp.o.d -o CMakeFiles/megahit_core.dir/src/sorting/kmsort_selector.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmsort_selector.cpp [ 27% 30/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/sorting/read_to_sdbg_s1.cpp.o -MF CMakeFiles/megahit_core.dir/src/sorting/read_to_sdbg_s1.cpp.o.d -o CMakeFiles/megahit_core.dir/src/sorting/read_to_sdbg_s1.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/read_to_sdbg_s1.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/read_to_sdbg_s1.cpp:22: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/read_to_sdbg.h:33: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.h:31: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 1 warning generated. [ 28% 31/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/sorting/read_to_sdbg_s2.cpp.o -MF CMakeFiles/megahit_core.dir/src/sorting/read_to_sdbg_s2.cpp.o.d -o CMakeFiles/megahit_core.dir/src/sorting/read_to_sdbg_s2.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/read_to_sdbg_s2.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/read_to_sdbg_s2.cpp:22: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/read_to_sdbg.h:33: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.h:31: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 1 warning generated. [ 29% 32/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/sorting/seq_to_sdbg.cpp.o -MF CMakeFiles/megahit_core.dir/src/sorting/seq_to_sdbg.cpp.o.d -o CMakeFiles/megahit_core.dir/src/sorting/seq_to_sdbg.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/seq_to_sdbg.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/seq_to_sdbg.cpp:30: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/async_sequence_reader.h:10: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 1 warning generated. [ 30% 33/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/tools/contigs_to_fastg.cpp.o -MF CMakeFiles/megahit_core.dir/src/tools/contigs_to_fastg.cpp.o.d -o CMakeFiles/megahit_core.dir/src/tools/contigs_to_fastg.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/tools/contigs_to_fastg.cpp [ 30% 34/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/tools/filter_by_len.cpp.o -MF CMakeFiles/megahit_core.dir/src/tools/filter_by_len.cpp.o.d -o CMakeFiles/megahit_core.dir/src/tools/filter_by_len.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/tools/filter_by_len.cpp [ 31% 35/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mbmi2 -DUSE_BMI2 -mpopcnt -MD -MT CMakeFiles/megahit_core.dir/src/tools/read_stat.cpp.o -MF CMakeFiles/megahit_core.dir/src/tools/read_stat.cpp.o.d -o CMakeFiles/megahit_core.dir/src/tools/read_stat.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/tools/read_stat.cpp [ 32% 36/110] : && /ccache/libexec/ccache/c++ -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -fstack-protector-strong CMakeFiles/megahit_core.dir/src/main.cpp.o CMakeFiles/megahit_core.dir/src/main_assemble.cpp.o CMakeFiles/megahit_core.dir/src/main_buildlib.cpp.o CMakeFiles/megahit_core.dir/src/main_iterate.cpp.o CMakeFiles/megahit_core.dir/src/main_local_assemble.cpp.o CMakeFiles/megahit_core.dir/src/main_sdbg_build.cpp.o CMakeFiles/megahit_core.dir/src/utils/options_description.cpp.o CMakeFiles/megahit_core.dir/src/assembly/bubble_remover.cpp.o CMakeFiles/megahit_core.dir/src/assembly/contig_output.cpp.o CMakeFiles/megahit_core.dir/src/assembly/low_depth_remover.cpp.o CMakeFiles/megahit_core.dir/src/assembly/sdbg_pruning.cpp.o CMakeFiles/megahit_core.dir/src/assembly/tip_remover.cpp.o CMakeFiles/megahit_core.dir/src/assembly/unitig_graph.cpp.o CMakeFiles/megahit_core.dir/src/assembly/weak_link_remover.cpp.o CMakeFiles/megahit_core.dir/src/idba/contig_graph.cpp.o CMakeFiles/megahit_core.dir/src/idba/contig_graph_branch_group.cpp.o CMakeFiles/megahit_core.dir/src/idba/hash_graph.cpp.o CMakeFiles/megahit_core.dir/src/idba/sequence.cpp.o CMakeFiles/megahit_core.dir/src/sdbg/sdbg_meta.cpp.o CMakeFiles/megahit_core.dir/src/sdbg/sdbg_raw_content.cpp.o CMakeFiles/megahit_core.dir/src/sdbg/sdbg_writer.cpp.o CMakeFiles/megahit_core.dir/src/localasm/hash_mapper.cpp.o CMakeFiles/megahit_core.dir/src/localasm/local_assemble.cpp.o CMakeFiles/megahit_core.dir/src/sequence/io/fastx_reader.cpp.o CMakeFiles/megahit_core.dir/src/sequence/io/paired_fastx_reader.cpp.o CMakeFiles/megahit_core.dir/src/sequence/io/sequence_lib.cpp.o CMakeFiles/megahit_core.dir/src/sorting/base_engine.cpp.o CMakeFiles/megahit_core.dir/src/sorting/kmer_counter.cpp.o CMakeFiles/megahit_core.dir/src/sorting/kmsort_selector.cpp.o CMakeFiles/megahit_core.dir/src/sorting/read_to_sdbg_s1.cpp.o CMakeFiles/megahit_core.dir/src/sorting/read_to_sdbg_s2.cpp.o CMakeFiles/megahit_core.dir/src/sorting/seq_to_sdbg.cpp.o CMakeFiles/megahit_core.dir/src/tools/contigs_to_fastg.cpp.o CMakeFiles/megahit_core.dir/src/tools/filter_by_len.cpp.o CMakeFiles/megahit_core.dir/src/tools/read_stat.cpp.o -o megahit_core -lz && : [ 33% 37/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/main.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/main.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/main.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main.cpp [ 34% 38/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/main_assemble.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/main_assemble.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/main_assemble.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_assemble.cpp [ 35% 39/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/main_buildlib.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/main_buildlib.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/main_buildlib.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_buildlib.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_buildlib.cpp:1: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.h:31: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 1 warning generated. [ 36% 40/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/main_iterate.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/main_iterate.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/main_iterate.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_iterate.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_iterate.cpp:38: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/async_sequence_reader.h:10: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 1 warning generated. [ 37% 41/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/main_local_assemble.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/main_local_assemble.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/main_local_assemble.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_local_assemble.cpp [ 38% 42/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/main_sdbg_build.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/main_sdbg_build.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/main_sdbg_build.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_sdbg_build.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_sdbg_build.cpp:29: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmer_counter.h:53:18: warning: class with destructor marked 'final' cannot be inherited from [-Wfinal-dtor-non-final-class] ~KmerCounter() final = default; ^ /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmer_counter.h:46:7: note: mark 'KmerCounter' as 'final' to silence this warning class KmerCounter : public BaseSequenceSortingEngine { ^ In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_sdbg_build.cpp:30: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/read_to_sdbg.h:33: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.h:31: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 2 warnings generated. [ 39% 43/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/utils/options_description.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/utils/options_description.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/utils/options_description.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/utils/options_description.cpp [ 40% 44/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/assembly/bubble_remover.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/assembly/bubble_remover.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/assembly/bubble_remover.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/assembly/bubble_remover.cpp [ 40% 45/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/assembly/contig_output.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/assembly/contig_output.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/assembly/contig_output.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/assembly/contig_output.cpp [ 41% 46/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/assembly/low_depth_remover.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/assembly/low_depth_remover.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/assembly/low_depth_remover.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/assembly/low_depth_remover.cpp [ 42% 47/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/assembly/sdbg_pruning.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/assembly/sdbg_pruning.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/assembly/sdbg_pruning.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/assembly/sdbg_pruning.cpp [ 43% 48/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/assembly/tip_remover.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/assembly/tip_remover.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/assembly/tip_remover.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/assembly/tip_remover.cpp [ 44% 49/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/assembly/unitig_graph.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/assembly/unitig_graph.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/assembly/unitig_graph.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/assembly/unitig_graph.cpp [ 45% 50/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/assembly/weak_link_remover.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/assembly/weak_link_remover.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/assembly/weak_link_remover.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/assembly/weak_link_remover.cpp [ 46% 51/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/idba/contig_graph.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/idba/contig_graph.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/idba/contig_graph.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/idba/contig_graph.cpp [ 47% 52/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/idba/contig_graph_branch_group.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/idba/contig_graph_branch_group.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/idba/contig_graph_branch_group.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/idba/contig_graph_branch_group.cpp [ 48% 53/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/idba/hash_graph.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/idba/hash_graph.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/idba/hash_graph.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/idba/hash_graph.cpp [ 49% 54/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/idba/sequence.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/idba/sequence.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/idba/sequence.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/idba/sequence.cpp [ 50% 55/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/sdbg/sdbg_meta.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/sdbg/sdbg_meta.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/sdbg/sdbg_meta.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sdbg/sdbg_meta.cpp [ 50% 56/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/sdbg/sdbg_raw_content.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/sdbg/sdbg_raw_content.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/sdbg/sdbg_raw_content.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sdbg/sdbg_raw_content.cpp /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sdbg/sdbg_raw_content.cpp:39:10: warning: variable 'file_offset' set but not used [-Wunused-but-set-variable] size_t file_offset = 0; ^ 1 warning generated. [ 51% 57/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/sdbg/sdbg_writer.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/sdbg/sdbg_writer.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/sdbg/sdbg_writer.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sdbg/sdbg_writer.cpp [ 52% 58/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/localasm/hash_mapper.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/localasm/hash_mapper.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/localasm/hash_mapper.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/localasm/hash_mapper.cpp [ 53% 59/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/localasm/local_assemble.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/localasm/local_assemble.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/localasm/local_assemble.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/localasm/local_assemble.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/localasm/local_assemble.cpp:19: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.h:31: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 1 warning generated. [ 54% 60/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/sequence/io/fastx_reader.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/sequence/io/fastx_reader.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/sequence/io/fastx_reader.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/fastx_reader.cpp [ 55% 61/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/sequence/io/paired_fastx_reader.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/sequence/io/paired_fastx_reader.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/sequence/io/paired_fastx_reader.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/paired_fastx_reader.cpp [ 56% 62/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/sequence/io/sequence_lib.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/sequence/io/sequence_lib.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/sequence/io/sequence_lib.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.cpp:5: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.h:31: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 1 warning generated. [ 57% 63/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/sorting/base_engine.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/sorting/base_engine.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/sorting/base_engine.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/base_engine.cpp [ 58% 64/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/sorting/kmer_counter.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/sorting/kmer_counter.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/sorting/kmer_counter.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmer_counter.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmer_counter.cpp:1: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmer_counter.h:53:18: warning: class with destructor marked 'final' cannot be inherited from [-Wfinal-dtor-non-final-class] ~KmerCounter() final = default; ^ /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmer_counter.h:46:7: note: mark 'KmerCounter' as 'final' to silence this warning class KmerCounter : public BaseSequenceSortingEngine { ^ In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmer_counter.cpp:6: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.h:31: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 2 warnings generated. [ 59% 65/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/sorting/kmsort_selector.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/sorting/kmsort_selector.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/sorting/kmsort_selector.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmsort_selector.cpp [ 60% 66/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/sorting/read_to_sdbg_s1.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/sorting/read_to_sdbg_s1.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/sorting/read_to_sdbg_s1.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/read_to_sdbg_s1.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/read_to_sdbg_s1.cpp:22: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/read_to_sdbg.h:33: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.h:31: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 1 warning generated. [ 60% 67/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/sorting/read_to_sdbg_s2.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/sorting/read_to_sdbg_s2.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/sorting/read_to_sdbg_s2.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/read_to_sdbg_s2.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/read_to_sdbg_s2.cpp:22: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/read_to_sdbg.h:33: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.h:31: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 1 warning generated. [ 61% 68/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/sorting/seq_to_sdbg.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/sorting/seq_to_sdbg.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/sorting/seq_to_sdbg.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/seq_to_sdbg.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/seq_to_sdbg.cpp:30: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/async_sequence_reader.h:10: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 1 warning generated. [ 62% 69/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/tools/contigs_to_fastg.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/tools/contigs_to_fastg.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/tools/contigs_to_fastg.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/tools/contigs_to_fastg.cpp [ 63% 70/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/tools/filter_by_len.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/tools/filter_by_len.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/tools/filter_by_len.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/tools/filter_by_len.cpp [ 64% 71/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -mpopcnt -MD -MT CMakeFiles/megahit_core_popcnt.dir/src/tools/read_stat.cpp.o -MF CMakeFiles/megahit_core_popcnt.dir/src/tools/read_stat.cpp.o.d -o CMakeFiles/megahit_core_popcnt.dir/src/tools/read_stat.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/tools/read_stat.cpp [ 65% 72/110] : && /ccache/libexec/ccache/c++ -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -fstack-protector-strong CMakeFiles/megahit_core_popcnt.dir/src/main.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/main_assemble.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/main_buildlib.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/main_iterate.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/main_local_assemble.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/main_sdbg_build.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/utils/options_description.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/assembly/bubble_remover.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/assembly/contig_output.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/assembly/low_depth_remover.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/assembly/sdbg_pruning.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/assembly/tip_remover.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/assembly/unitig_graph.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/assembly/weak_link_remover.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/idba/contig_graph.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/idba/contig_graph_branch_group.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/idba/hash_graph.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/idba/sequence.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/sdbg/sdbg_meta.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/sdbg/sdbg_raw_content.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/sdbg/sdbg_writer.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/localasm/hash_mapper.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/localasm/local_assemble.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/sequence/io/fastx_reader.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/sequence/io/paired_fastx_reader.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/sequence/io/sequence_lib.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/sorting/base_engine.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/sorting/kmer_counter.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/sorting/kmsort_selector.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/sorting/read_to_sdbg_s1.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/sorting/read_to_sdbg_s2.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/sorting/seq_to_sdbg.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/tools/contigs_to_fastg.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/tools/filter_by_len.cpp.o CMakeFiles/megahit_core_popcnt.dir/src/tools/read_stat.cpp.o -o megahit_core_popcnt -lz && : [ 66% 73/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/main.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/main.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/main.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main.cpp [ 67% 74/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/main_assemble.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/main_assemble.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/main_assemble.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_assemble.cpp [ 68% 75/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/main_buildlib.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/main_buildlib.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/main_buildlib.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_buildlib.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_buildlib.cpp:1: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.h:31: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 1 warning generated. [ 69% 76/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/main_iterate.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/main_iterate.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/main_iterate.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_iterate.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_iterate.cpp:38: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/async_sequence_reader.h:10: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 1 warning generated. [ 70% 77/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/main_local_assemble.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/main_local_assemble.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/main_local_assemble.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_local_assemble.cpp [ 70% 78/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/main_sdbg_build.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/main_sdbg_build.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/main_sdbg_build.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_sdbg_build.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_sdbg_build.cpp:29: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmer_counter.h:53:18: warning: class with destructor marked 'final' cannot be inherited from [-Wfinal-dtor-non-final-class] ~KmerCounter() final = default; ^ /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmer_counter.h:46:7: note: mark 'KmerCounter' as 'final' to silence this warning class KmerCounter : public BaseSequenceSortingEngine { ^ In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/main_sdbg_build.cpp:30: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/read_to_sdbg.h:33: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.h:31: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 2 warnings generated. [ 71% 79/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/utils/options_description.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/utils/options_description.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/utils/options_description.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/utils/options_description.cpp [ 72% 80/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/bubble_remover.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/bubble_remover.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/bubble_remover.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/assembly/bubble_remover.cpp [ 73% 81/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/contig_output.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/contig_output.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/contig_output.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/assembly/contig_output.cpp [ 74% 82/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/low_depth_remover.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/low_depth_remover.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/low_depth_remover.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/assembly/low_depth_remover.cpp [ 75% 83/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/sdbg_pruning.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/sdbg_pruning.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/sdbg_pruning.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/assembly/sdbg_pruning.cpp [ 76% 84/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/tip_remover.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/tip_remover.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/tip_remover.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/assembly/tip_remover.cpp [ 77% 85/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/unitig_graph.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/unitig_graph.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/unitig_graph.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/assembly/unitig_graph.cpp [ 78% 86/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/weak_link_remover.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/weak_link_remover.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/weak_link_remover.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/assembly/weak_link_remover.cpp [ 79% 87/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/idba/contig_graph.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/idba/contig_graph.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/idba/contig_graph.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/idba/contig_graph.cpp [ 80% 88/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/idba/contig_graph_branch_group.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/idba/contig_graph_branch_group.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/idba/contig_graph_branch_group.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/idba/contig_graph_branch_group.cpp [ 80% 89/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/idba/hash_graph.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/idba/hash_graph.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/idba/hash_graph.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/idba/hash_graph.cpp [ 81% 90/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/idba/sequence.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/idba/sequence.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/idba/sequence.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/idba/sequence.cpp [ 82% 91/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/sdbg/sdbg_meta.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/sdbg/sdbg_meta.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/sdbg/sdbg_meta.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sdbg/sdbg_meta.cpp [ 83% 92/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/sdbg/sdbg_raw_content.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/sdbg/sdbg_raw_content.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/sdbg/sdbg_raw_content.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sdbg/sdbg_raw_content.cpp /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sdbg/sdbg_raw_content.cpp:39:10: warning: variable 'file_offset' set but not used [-Wunused-but-set-variable] size_t file_offset = 0; ^ 1 warning generated. [ 84% 93/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/sdbg/sdbg_writer.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/sdbg/sdbg_writer.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/sdbg/sdbg_writer.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sdbg/sdbg_writer.cpp [ 85% 94/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/localasm/hash_mapper.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/localasm/hash_mapper.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/localasm/hash_mapper.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/localasm/hash_mapper.cpp [ 86% 95/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/localasm/local_assemble.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/localasm/local_assemble.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/localasm/local_assemble.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/localasm/local_assemble.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/localasm/local_assemble.cpp:19: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.h:31: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 1 warning generated. [ 87% 96/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/sequence/io/fastx_reader.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/sequence/io/fastx_reader.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/sequence/io/fastx_reader.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/fastx_reader.cpp [ 88% 97/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/sequence/io/paired_fastx_reader.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/sequence/io/paired_fastx_reader.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/sequence/io/paired_fastx_reader.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/paired_fastx_reader.cpp [ 89% 98/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/sequence/io/sequence_lib.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/sequence/io/sequence_lib.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/sequence/io/sequence_lib.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.cpp:5: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.h:31: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 1 warning generated. [ 90% 99/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/base_engine.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/base_engine.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/base_engine.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/base_engine.cpp [ 90% 100/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/kmer_counter.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/kmer_counter.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/kmer_counter.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmer_counter.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmer_counter.cpp:1: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmer_counter.h:53:18: warning: class with destructor marked 'final' cannot be inherited from [-Wfinal-dtor-non-final-class] ~KmerCounter() final = default; ^ /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmer_counter.h:46:7: note: mark 'KmerCounter' as 'final' to silence this warning class KmerCounter : public BaseSequenceSortingEngine { ^ In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmer_counter.cpp:6: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.h:31: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 2 warnings generated. [ 91% 101/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/kmsort_selector.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/kmsort_selector.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/kmsort_selector.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/kmsort_selector.cpp [ 92% 102/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/read_to_sdbg_s1.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/read_to_sdbg_s1.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/read_to_sdbg_s1.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/read_to_sdbg_s1.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/read_to_sdbg_s1.cpp:22: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/read_to_sdbg.h:33: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.h:31: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 1 warning generated. [ 93% 103/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/read_to_sdbg_s2.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/read_to_sdbg_s2.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/read_to_sdbg_s2.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/read_to_sdbg_s2.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/read_to_sdbg_s2.cpp:22: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/read_to_sdbg.h:33: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/sequence_lib.h:31: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 1 warning generated. [ 94% 104/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/seq_to_sdbg.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/seq_to_sdbg.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/seq_to_sdbg.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/seq_to_sdbg.cpp In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sorting/seq_to_sdbg.cpp:30: In file included from /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/async_sequence_reader.h:10: /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/sequence/io/binary_reader.h:26:13: warning: variable 'num_bases' set but not used [-Wunused-but-set-variable] int64_t num_bases = 0; ^ 1 warning generated. [ 95% 105/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/tools/contigs_to_fastg.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/tools/contigs_to_fastg.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/tools/contigs_to_fastg.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/tools/contigs_to_fastg.cpp [ 96% 106/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/tools/filter_by_len.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/tools/filter_by_len.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/tools/filter_by_len.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/tools/filter_by_len.cpp [ 97% 107/110] /ccache/libexec/ccache/c++ -I/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/megahit_core_no_hw_accel.dir/src/tools/read_stat.cpp.o -MF CMakeFiles/megahit_core_no_hw_accel.dir/src/tools/read_stat.cpp.o.d -o CMakeFiles/megahit_core_no_hw_accel.dir/src/tools/read_stat.cpp.o -c /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/tools/read_stat.cpp [ 98% 108/110] : && /ccache/libexec/ccache/c++ -O2 -pipe -pthread -fstack-protector-strong -fno-strict-aliasing -fopenmp=libomp -DXXH_INLINE_ALL -ftemplate-depth=3000 -Wall -Wno-unused-function -D__XROOT__='"/wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src"' -DNDEBUG -fstack-protector-strong CMakeFiles/megahit_core_no_hw_accel.dir/src/main.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/main_assemble.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/main_buildlib.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/main_iterate.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/main_local_assemble.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/main_sdbg_build.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/utils/options_description.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/bubble_remover.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/contig_output.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/low_depth_remover.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/sdbg_pruning.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/tip_remover.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/unitig_graph.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/assembly/weak_link_remover.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/idba/contig_graph.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/idba/contig_graph_branch_group.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/idba/hash_graph.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/idba/sequence.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/sdbg/sdbg_meta.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/sdbg/sdbg_raw_content.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/sdbg/sdbg_writer.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/localasm/hash_mapper.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/localasm/local_assemble.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/sequence/io/fastx_reader.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/sequence/io/paired_fastx_reader.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/sequence/io/sequence_lib.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/base_engine.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/kmer_counter.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/kmsort_selector.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/read_to_sdbg_s1.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/read_to_sdbg_s2.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/sorting/seq_to_sdbg.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/tools/contigs_to_fastg.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/tools/filter_by_len.cpp.o CMakeFiles/megahit_core_no_hw_accel.dir/src/tools/read_stat.cpp.o -o megahit_core_no_hw_accel -lz && : [ 99% 109/110] cd /wrkdirs/usr/ports/biology/megahit/work/.build && /usr/local/bin/cmake -E create_symlink megahit_core_no_hw_accel megahit_toolkit [100% 110/110] cd /wrkdirs/usr/ports/biology/megahit/work/.build && cp /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/megahit . =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> megahit-1.2.9_1 depends on file: /usr/local/bin/python3.9 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for megahit-1.2.9_1 ===> Generating temporary packing list [ 33% 1/3] cd /wrkdirs/usr/ports/biology/megahit/work/.build && /usr/local/bin/cmake -E create_symlink megahit_core_no_hw_accel megahit_toolkit [ 66% 2/3] cd /wrkdirs/usr/ports/biology/megahit/work/.build && cp /wrkdirs/usr/ports/biology/megahit/work/megahit-1.2.9/src/megahit . [ 66% 3/3] cd /wrkdirs/usr/ports/biology/megahit/work/.build && /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /wrkdirs/usr/ports/biology/megahit/work/stage/usr/local/bin/megahit_core -- Installing: /wrkdirs/usr/ports/biology/megahit/work/stage/usr/local/bin/megahit_core_popcnt -- Installing: /wrkdirs/usr/ports/biology/megahit/work/stage/usr/local/bin/megahit_core_no_hw_accel -- Installing: /wrkdirs/usr/ports/biology/megahit/work/stage/usr/local/bin/megahit -- Installing: /wrkdirs/usr/ports/biology/megahit/work/stage/usr/local/bin/megahit_toolkit -- Installing: /wrkdirs/usr/ports/biology/megahit/work/stage/usr/local/share/megahit/test_data -- Installing: /wrkdirs/usr/ports/biology/megahit/work/stage/usr/local/share/megahit/test_data/r2.il.fa.bz2 -- Installing: /wrkdirs/usr/ports/biology/megahit/work/stage/usr/local/share/megahit/test_data/empty.fa -- Installing: /wrkdirs/usr/ports/biology/megahit/work/stage/usr/local/share/megahit/test_data/r3_2.fa -- Installing: /wrkdirs/usr/ports/biology/megahit/work/stage/usr/local/share/megahit/test_data/r4.fa -- Installing: /wrkdirs/usr/ports/biology/megahit/work/stage/usr/local/share/megahit/test_data/loop.fa -- Installing: /wrkdirs/usr/ports/biology/megahit/work/stage/usr/local/share/megahit/test_data/r1.il.fa.gz -- Installing: /wrkdirs/usr/ports/biology/megahit/work/stage/usr/local/share/megahit/test_data/ref.fa -- Installing: /wrkdirs/usr/ports/biology/megahit/work/stage/usr/local/share/megahit/test_data/r3_1.fa -- Installing: /wrkdirs/usr/ports/biology/megahit/work/stage/usr/local/share/megahit/test_data/generate_random_fasta.py ====> 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=2024-04-04T19:10:04+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=c014f9c79a' '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 megahit-1.2.9_1 ===> Building megahit-1.2.9_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for megahit-1.2.9_1 build of biology/megahit | megahit-1.2.9_1 ended at Thu Apr 4 20:21:33 BST 2024 build time: 00:11:29