------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.1 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- ===> The following configuration options are available for hyphy-2.5.31: AVX=off: Advanced vector extensions support ===> Use 'make config' to modify these settings SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/hyphy XDG_CONFIG_HOME=/construction/biology/hyphy HOME=/construction/biology/hyphy TMPDIR="/tmp" PATH=/construction/biology/hyphy/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 CMAKE_PREFIX_PATH="/usr/local" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- OPENSSLBASE=/usr/local OPENSSLDIR=/usr/local/openssl OPENSSLINC=/usr/local/include OPENSSLLIB=/usr/local/lib OPENSSLRPATH=/usr/local/lib XDG_DATA_HOME=/construction/biology/hyphy XDG_CONFIG_HOME=/construction/biology/hyphy HOME=/construction/biology/hyphy TMPDIR="/tmp" PATH=/construction/biology/hyphy/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -Wl,-rpath,/usr/local/lib -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/hyphy/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- CMAKE_BUILD_TYPE="release" OSREL=6.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/hyphy" EXAMPLESDIR="share/examples/hyphy" DATADIR="share/hyphy" WWWDIR="www/hyphy" ETCDIR="etc/hyphy" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/hyphy DOCSDIR=/usr/local/share/doc/hyphy EXAMPLESDIR=/usr/local/share/examples/hyphy WWWDIR=/usr/local/www/hyphy ETCDIR=/usr/local/etc/hyphy SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600102 OSVERSION=9999999 OSREL=6.1 _OSRELEASE=6.1-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/libnghttp2-1.43.0.txz Installing /packages/All/ca_root_nss-3.63.txz ===== Message from ca_root_nss-3.63: -- FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem Installing /packages/All/openssl-1.1.1l,1.txz Installing /packages/All/curl-7.78.0.txz Installing /packages/All/expat-2.4.1.txz Installing /packages/All/libuv-1.41.0.txz Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/rhash-1.4.1.txz Installing /packages/All/liblz4-1.9.3,1.txz Installing /packages/All/libarchive-3.5.1,1.txz Installing /packages/All/ncurses-6.2.20210626.txz ===== Message from ncurses-6.2.20210626: -- { type: install message: < hyphy-2.5.31 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> hyphy-2.5.31 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by hyphy-2.5.31 for building SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> hyphy-2.5.31 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by hyphy-2.5.31 for building => SHA256 Checksum OK for veg-hyphy-2.5.31_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> hyphy-2.5.31 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by hyphy-2.5.31 for building ===> Extracting for hyphy-2.5.31 => SHA256 Checksum OK for veg-hyphy-2.5.31_GH0.tar.gz. Extracted Memory Use: 28.79M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for hyphy-2.5.31 ===> Applying ports patches for hyphy-2.5.31 from /xports/biology/hyphy/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> hyphy-2.5.31 depends on file: /usr/local/bin/cmake - found ===> hyphy-2.5.31 depends on file: /usr/local/lib/libcrypto.so.11 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> hyphy-2.5.31 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> hyphy-2.5.31 depends on file: /usr/local/bin/cmake - found ===> hyphy-2.5.31 depends on file: /usr/local/lib/libcrypto.so.11 - found ===> hyphy-2.5.31 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> Configuring for hyphy-2.5.31 ===> Performing out-of-source build /bin/mkdir -p /construction/biology/hyphy/.build -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAVE_SSE3_EXTENSIONS -- Performing Test HAVE_SSE3_EXTENSIONS - Success Set compiler flags to -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found CURL: /usr/local/lib/libcurl.so (found version "7.78.0") /usr/local/lib/libcurl.so -- Found ZLIB: /usr/lib/libz.so (found suitable version "1.2.11", minimum required is "1.2.9") Node not installed; API documentation will not be generated -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /construction/biology/hyphy/.build SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for hyphy-2.5.31 /usr/local/bin/cmake -S/construction/biology/hyphy/hyphy-2.5.31 -B/construction/biology/hyphy/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/biology/hyphy/.build/CMakeFiles /construction/biology/hyphy/.build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all --- CMakeFiles/hyphy.dir/all --- /usr/bin/make -f CMakeFiles/hyphy.dir/build.make CMakeFiles/hyphy.dir/depend --- CMakeFiles/hyphy.dir/depend --- cd 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CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o --- [ 7%] Building CXX object CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o --- CMakeFiles/hyphy.dir/src/core/alignment.cpp.o --- [ 7%] Building CXX object CMakeFiles/hyphy.dir/src/core/alignment.cpp.o --- CMakeFiles/hyphy.dir/src/core/avllist.cpp.o --- [ 7%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllist.cpp.o --- CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o --- [ 7%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o --- CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o --- [ 11%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o --- CMakeFiles/hyphy.dir/src/core/alignment.cpp.o --- /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include 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-I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/avllist.cpp.o -MF CMakeFiles/hyphy.dir/src/core/avllist.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/avllist.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/avllist.cpp --- CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o --- /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ 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-I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o -MF CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/avllistx_iterator.cpp --- CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o --- [ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o -MF CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/baseobj.cpp --- CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o --- [ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o -MF 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-mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o -MF CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/batchlanhelpers.cpp --- CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o --- [ 19%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o -MF CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/batchlanruntime.cpp --- CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o --- [ 23%] Building CXX object CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o -MF CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/calcnode.cpp --- CMakeFiles/hyphy.dir/src/core/category.cpp.o --- [ 23%] Building CXX object CMakeFiles/hyphy.dir/src/core/category.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/category.cpp.o -MF CMakeFiles/hyphy.dir/src/core/category.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/category.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/category.cpp --- CMakeFiles/hyphy.dir/src/core/constant.cpp.o --- [ 23%] Building CXX object CMakeFiles/hyphy.dir/src/core/constant.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/constant.cpp.o -MF CMakeFiles/hyphy.dir/src/core/constant.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/constant.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/constant.cpp --- CMakeFiles/hyphy.dir/src/core/dataset.cpp.o --- [ 26%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/dataset.cpp.o -MF CMakeFiles/hyphy.dir/src/core/dataset.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/dataset.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/dataset.cpp --- CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o --- [ 26%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o -MF CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/dataset_filter.cpp--- CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o --- [ 26%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o -MF CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/dataset_filter_numeric.cpp --- CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o --- [ 30%] Building CXX object CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o -MF CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/fisher_exact.cpp --- CMakeFiles/hyphy.dir/src/core/formula.cpp.o --- [ 30%] Building CXX object CMakeFiles/hyphy.dir/src/core/formula.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/formula.cpp.o -MF CMakeFiles/hyphy.dir/src/core/formula.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/formula.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/formula.cpp --- CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o --- [ 34%] Building CXX object CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o -MF CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/formula_parsing_context.cpp --- CMakeFiles/hyphy.dir/src/core/fstring.cpp.o --- [ 34%] Building CXX object CMakeFiles/hyphy.dir/src/core/fstring.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/fstring.cpp.o -MF CMakeFiles/hyphy.dir/src/core/fstring.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/fstring.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/fstring.cpp --- CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o --- --- CMakeFiles/hyphy.dir/src/core/global_things.cpp.o --- --- CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o --- [ 34%] Building CXX object CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o -MF CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/global_object_lists.cpp --- CMakeFiles/hyphy.dir/src/core/global_things.cpp.o --- [ 38%] Building CXX object CMakeFiles/hyphy.dir/src/core/global_things.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/global_things.cpp.o -MF CMakeFiles/hyphy.dir/src/core/global_things.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/global_things.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/global_things.cpp --- CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o --- [ 38%] Building CXX object CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o -MF CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/hbl_env.cpp --- CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o --- [ 38%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o -MF CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/likefunc.cpp --- CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o --- [ 42%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o -MF CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/likefunc2.cpp --- CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o --- [ 42%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o -MF CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/likefuncocl.cpp --- CMakeFiles/hyphy.dir/src/core/list.cpp.o --- [ 46%] Building CXX object CMakeFiles/hyphy.dir/src/core/list.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/list.cpp.o -MF CMakeFiles/hyphy.dir/src/core/list.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/list.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/list.cpp --- CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o --- [ 46%] Building CXX object CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o -MF CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/mathobj.cpp --- CMakeFiles/hyphy.dir/src/core/matrix.cpp.o --- [ 46%] Building CXX object CMakeFiles/hyphy.dir/src/core/matrix.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/matrix.cpp.o -MF CMakeFiles/hyphy.dir/src/core/matrix.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/matrix.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/matrix.cpp --- CMakeFiles/hyphy.dir/src/core/nexus.cpp.o --- [ 50%] Building CXX object CMakeFiles/hyphy.dir/src/core/nexus.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/nexus.cpp.o -MF CMakeFiles/hyphy.dir/src/core/nexus.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/nexus.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/nexus.cpp --- CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o --- [ 50%] Building CXX object CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o -MF CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/ntuplestorage.cpp --- CMakeFiles/hyphy.dir/src/core/operation.cpp.o --- [ 50%] Building CXX object CMakeFiles/hyphy.dir/src/core/operation.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/operation.cpp.o -MF CMakeFiles/hyphy.dir/src/core/operation.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/operation.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/operation.cpp --- CMakeFiles/hyphy.dir/src/core/parser.cpp.o --- --- CMakeFiles/hyphy.dir/src/core/parser2.cpp.o --- [ 53%] Building CXX object CMakeFiles/hyphy.dir/src/core/parser2.cpp.o --- CMakeFiles/hyphy.dir/src/core/parser.cpp.o --- [ 53%] Building CXX object CMakeFiles/hyphy.dir/src/core/parser.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/parser.cpp.o -MF CMakeFiles/hyphy.dir/src/core/parser.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/parser.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/parser.cpp --- CMakeFiles/hyphy.dir/src/core/parser2.cpp.o --- /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/parser2.cpp.o -MF CMakeFiles/hyphy.dir/src/core/parser2.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/parser2.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/parser2.cpp --- CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o --- [ 57%] Building CXX object CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o -MF CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/polynoml.cpp --- CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o --- [ 57%] Building CXX object CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o -MF CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/simplelist.cpp --- CMakeFiles/hyphy.dir/src/core/site.cpp.o --- [ 57%] Building CXX object CMakeFiles/hyphy.dir/src/core/site.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/site.cpp.o -MF CMakeFiles/hyphy.dir/src/core/site.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/site.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/site.cpp --- CMakeFiles/hyphy.dir/src/core/stack.cpp.o --- [ 61%] Building CXX object CMakeFiles/hyphy.dir/src/core/stack.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/stack.cpp.o -MF CMakeFiles/hyphy.dir/src/core/stack.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/stack.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/stack.cpp --- CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o --- [ 61%] Building CXX object CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o -MF CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/string_buffer.cpp --- CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o --- [ 61%] Building CXX object CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o -MF CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/string_file_wrapper.cpp --- CMakeFiles/hyphy.dir/src/core/strings.cpp.o --- [ 65%] Building CXX object CMakeFiles/hyphy.dir/src/core/strings.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/strings.cpp.o -MF CMakeFiles/hyphy.dir/src/core/strings.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/strings.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/strings.cpp --- CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o --- [ 65%] Building CXX object CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o -MF CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/time_difference.cpp --- CMakeFiles/hyphy.dir/src/core/topology.cpp.o --- [ 69%] Building CXX object CMakeFiles/hyphy.dir/src/core/topology.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/topology.cpp.o -MF CMakeFiles/hyphy.dir/src/core/topology.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/topology.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/topology.cpp --- CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o --- [ 69%] Building CXX object CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o -MF CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/translation_table.cpp --- CMakeFiles/hyphy.dir/src/core/tree.cpp.o --- [ 69%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/tree.cpp.o -MF CMakeFiles/hyphy.dir/src/core/tree.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/tree.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/tree.cpp --- CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o --- [ 73%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o -MF CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/tree_evaluator.cpp--- CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o --- [ 73%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o -MF CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/tree_iterator.cpp --- CMakeFiles/hyphy.dir/src/core/trie.cpp.o --- [ 73%] Building CXX object CMakeFiles/hyphy.dir/src/core/trie.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/trie.cpp.o -MF CMakeFiles/hyphy.dir/src/core/trie.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/trie.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/trie.cpp --- CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o --- [ 76%] Building CXX object CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o -MF CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/trie_iterator.cpp --- CMakeFiles/hyphy.dir/src/core/variable.cpp.o --- [ 76%] Building CXX object CMakeFiles/hyphy.dir/src/core/variable.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/construction/biology/hyphy/hyphy-2.5.31/src/core/include -I/construction/biology/hyphy/hyphy-2.5.31/src/contrib -I/construction/biology/hyphy/hyphy-2.5.31/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.31/src/new/include -I/construction/biology/hyphy/hyphy-2.5.31/contrib/SQLite-3.8.2 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -std=c++14 -mno-avx -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/variable.cpp.o -MF CMakeFiles/hyphy.dir/src/core/variable.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/variable.cpp.o -c /construction/biology/hyphy/hyphy-2.5.31/src/core/variable.cpp --- CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o --- [ 80%] Building CXX object CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS 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------------------------------------------------------------------------------- ===> Building package for hyphy-2.5.31 file sizes/checksums [436]: 0% file sizes/checksums [436]: 22% file sizes/checksums [436]: 45% file sizes/checksums [436]: 68% file sizes/checksums [436]: 91% file sizes/checksums [436]: 100% packing files [436]: 0% packing files [436]: 22% packing files [436]: 45% packing files [436]: 68% packing files [436]: 91% packing files [436]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:15 TOTAL TIME 00:04:25