=> Building biology/hyphy Started : Thursday, 30 AUG 2018 at 13:01:44 UTC Platform: 5.3-DEVELOPMENT DragonFly 5.3-DEVELOPMENT #140: Wed Aug 29 22:06:30 PDT 2018 root@test.backplane.com:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.3-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.3-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/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=gcc50 CMAKE_PREFIX_PATH="/usr/local" -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- 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=gcc50 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" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/hyphy/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" CMAKE_BUILD_TYPE="release" OSREL=5.3 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" -------------------------------------------------- -- 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 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=LiveSystem USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=12 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500316 OSVERSION=9999999 OSREL=5.3 _OSRELEASE=5.3-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License MIT accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> hyphy-2.3.13 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz Installing pkg-1.10.5_1... Extracting pkg-1.10.5_1: .......... done ===> hyphy-2.3.13 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of hyphy-2.3.13 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by hyphy-2.3.13 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by hyphy-2.3.13 for building => SHA256 Checksum OK for veg-hyphy-2.3.13_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by hyphy-2.3.13 for building ===> Extracting for hyphy-2.3.13 => SHA256 Checksum OK for veg-hyphy-2.3.13_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for hyphy-2.3.13 ===> Applying ports patches for hyphy-2.3.13 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> hyphy-2.3.13 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.11.4_1.txz Installing cmake-3.11.4_1... `-- Installing curl-7.60.0... | `-- Installing ca_root_nss-3.38... | `-- Extracting ca_root_nss-3.38: ........ done | `-- Installing krb5-1.16.1_5... | | `-- Installing gettext-runtime-0.19.8.1_1... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: .... done | | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done | | `-- Installing libressl-2.7.4... | | `-- Extracting libressl-2.7.4: .......... done | | `-- Installing pkgconf-1.4.2,1... | | `-- Extracting pkgconf-1.4.2,1: .......... done | | `-- Installing readline-7.0.3_1... | | `-- Installing ncurses-6.0.0s20171223_1... | | `-- Extracting ncurses-6.0.0s20171223_1: .......... done | | `-- Extracting readline-7.0.3_1: .......... done | `-- Extracting krb5-1.16.1_5: .......... done | `-- Installing libnghttp2-1.32.0... | `-- Extracting libnghttp2-1.32.0: .......... done `-- Extracting curl-7.60.0: .......... done `-- Installing expat-2.2.5... `-- Extracting expat-2.2.5: .......... done `-- Installing jsoncpp-1.8.1_3... `-- Extracting jsoncpp-1.8.1_3: .......... done `-- Installing libarchive-3.3.2,1... | `-- Installing liblz4-1.8.2,1... | `-- Extracting liblz4-1.8.2,1: .......... done | `-- Installing lzo2-2.10_1... | `-- Extracting lzo2-2.10_1: .......... done `-- Extracting libarchive-3.3.2,1: .......... done `-- Installing libuv-1.21.0... `-- Extracting libuv-1.21.0: .......... done `-- Installing rhash-1.3.5... `-- Extracting rhash-1.3.5: .......... done Extracting cmake-3.11.4_1: .......... done Message from ca_root_nss-3.38: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** ===> hyphy-2.3.13 depends on file: /usr/local/bin/cmake - found ===> Returning to build of hyphy-2.3.13 ===> hyphy-2.3.13 depends on file: /usr/local/lib/libcrypto.so.43 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> hyphy-2.3.13 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for hyphy-2.3.13 ===> Performing out-of-source build /bin/mkdir -p /construction/biology/hyphy/.build -- The C compiler identification is GNU 5.4.1 -- The CXX compiler identification is GNU 5.4.1 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAVE_AVX_EXTENSIONS -- Performing Test HAVE_AVX_EXTENSIONS - Success Set compiler flags to -fsigned-char -O3 -std=gnu++14 -march=corei7-avx -mtune=corei7-avx -- Found OpenMP_C: -fopenmp (found version "4.0") -- Found OpenMP_CXX: -fopenmp (found version "4.0") -- Found OpenMP: TRUE (found version "4.0") -- Found CURL: /usr/local/lib/libcurl.so (found version "7.60.0") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Looking for pthread.h -- Looking for pthread.h - found -- Found Threads: TRUE -- Looking for CL_VERSION_2_2 -- Looking for CL_VERSION_2_2 - not found -- Looking for CL_VERSION_2_1 -- Looking for CL_VERSION_2_1 - not found -- Looking for CL_VERSION_2_0 -- Looking for CL_VERSION_2_0 - not found -- Looking for CL_VERSION_1_2 -- Looking for CL_VERSION_1_2 - not found -- Looking for CL_VERSION_1_1 -- Looking for CL_VERSION_1_1 - not found -- Looking for CL_VERSION_1_0 -- Looking for CL_VERSION_1_0 - not found -- Could NOT find OpenCL (missing: OpenCL_LIBRARY OpenCL_INCLUDE_DIR) -- 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_CXX_FLAGS_DEBUG CMAKE_C_FLAGS_DEBUG CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS -- Build files have been written to: /construction/biology/hyphy/.build -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for hyphy-2.3.13 /usr/local/bin/cmake -H/construction/biology/hyphy/hyphy-2.3.13 -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/HYPHYMP.dir/all --- /usr/bin/make -f CMakeFiles/HYPHYMP.dir/build.make CMakeFiles/HYPHYMP.dir/depend --- CMakeFiles/HYPHYMP.dir/depend --- cd /construction/biology/hyphy/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hyphy/hyphy-2.3.13 /construction/biology/hyphy/hyphy-2.3.13 /construction/biology/hyphy/.build /construction/biology/hyphy/.build /construction/biology/hyphy/.build/CMakeFiles/HYPHYMP.dir/DependInfo.cmake Scanning dependencies of target HYPHYMP /usr/bin/make -f CMakeFiles/HYPHYMP.dir/build.make CMakeFiles/HYPHYMP.dir/build --- CMakeFiles/HYPHYMP.dir/src/core/_hyExecutionContext.cpp.o --- --- CMakeFiles/HYPHYMP.dir/src/core/alignment.cpp.o --- --- CMakeFiles/HYPHYMP.dir/src/core/avllist.cpp.o --- --- CMakeFiles/HYPHYMP.dir/src/core/avllistx.cpp.o --- --- CMakeFiles/HYPHYMP.dir/src/core/avllistxl.cpp.o --- --- CMakeFiles/HYPHYMP.dir/src/core/avllistxl_iterator.cpp.o --- --- CMakeFiles/HYPHYMP.dir/src/core/baseobj.cpp.o --- --- CMakeFiles/HYPHYMP.dir/src/core/batchlan.cpp.o --- --- CMakeFiles/HYPHYMP.dir/src/core/batchlan2.cpp.o --- --- CMakeFiles/HYPHYMP.dir/src/core/batchlanhelpers.cpp.o --- --- CMakeFiles/HYPHYMP.dir/src/core/batchlanruntime.cpp.o --- --- CMakeFiles/HYPHYMP.dir/src/core/calcnode.cpp.o --- --- CMakeFiles/HYPHYMP.dir/src/core/alignment.cpp.o --- [ 0%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/alignment.cpp.o --- CMakeFiles/HYPHYMP.dir/src/core/avllistxl_iterator.cpp.o --- [ 6%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/avllistxl_iterator.cpp.o --- CMakeFiles/HYPHYMP.dir/src/core/avllist.cpp.o --- [ 6%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/avllist.cpp.o --- CMakeFiles/HYPHYMP.dir/src/core/_hyExecutionContext.cpp.o --- [ 9%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/_hyExecutionContext.cpp.o --- CMakeFiles/HYPHYMP.dir/src/core/avllistx.cpp.o --- [ 9%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/avllistx.cpp.o --- CMakeFiles/HYPHYMP.dir/src/core/baseobj.cpp.o --- [ 9%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/baseobj.cpp.o --- CMakeFiles/HYPHYMP.dir/src/core/avllistxl.cpp.o --- [ 12%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/avllistxl.cpp.o --- CMakeFiles/HYPHYMP.dir/src/core/batchlan.cpp.o --- [ 15%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/batchlan.cpp.o --- CMakeFiles/HYPHYMP.dir/src/core/alignment.cpp.o --- /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHY_64__ -D__MP2__ -D__MP__ -D__UNIX__ -I/construction/biology/hyphy/hyphy-2.3.13/src/core/include -I/construction/biology/hyphy/hyphy-2.3.13/src/lib/Link -I/construction/biology/hyphy/hyphy-2.3.13/src/new/include -I/construction/biology/hyphy/hyphy-2.3.13/contrib/SQLite-3.8.2 -I/construction/biology/hyphy/hyphy-2.3.13/contrib/gtest-1.7.0/include -I/construction/biology/hyphy/hyphy-2.3.13/tests/gtests -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=gnu++14 -march=corei7-avx -mtune=corei7-avx -w -fopenmp -w 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CMakeFiles/HYPHYMP.dir/src/core/batchlanhelpers.cpp.o --- [ 21%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/batchlanhelpers.cpp.o --- CMakeFiles/HYPHYMP.dir/src/core/calcnode.cpp.o --- /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHY_64__ -D__MP2__ -D__MP__ -D__UNIX__ -I/construction/biology/hyphy/hyphy-2.3.13/src/core/include -I/construction/biology/hyphy/hyphy-2.3.13/src/lib/Link -I/construction/biology/hyphy/hyphy-2.3.13/src/new/include -I/construction/biology/hyphy/hyphy-2.3.13/contrib/SQLite-3.8.2 -I/construction/biology/hyphy/hyphy-2.3.13/contrib/gtest-1.7.0/include -I/construction/biology/hyphy/hyphy-2.3.13/tests/gtests -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=gnu++14 -march=corei7-avx -mtune=corei7-avx 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-I/construction/biology/hyphy/hyphy-2.3.13/contrib/SQLite-3.8.2 -I/construction/biology/hyphy/hyphy-2.3.13/contrib/gtest-1.7.0/include -I/construction/biology/hyphy/hyphy-2.3.13/tests/gtests -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=gnu++14 -march=corei7-avx -mtune=corei7-avx -w -fopenmp -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMP.dir/src/core/regex.cpp.o -c /construction/biology/hyphy/hyphy-2.3.13/src/core/regex.cpp --- CMakeFiles/HYPHYMP.dir/src/core/sequence.cpp.o --- [ 65%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/sequence.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHY_64__ -D__MP2__ -D__MP__ -D__UNIX__ -I/construction/biology/hyphy/hyphy-2.3.13/src/core/include -I/construction/biology/hyphy/hyphy-2.3.13/src/lib/Link -I/construction/biology/hyphy/hyphy-2.3.13/src/new/include -I/construction/biology/hyphy/hyphy-2.3.13/contrib/SQLite-3.8.2 -I/construction/biology/hyphy/hyphy-2.3.13/contrib/gtest-1.7.0/include -I/construction/biology/hyphy/hyphy-2.3.13/tests/gtests -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=gnu++14 -march=corei7-avx -mtune=corei7-avx -w -fopenmp -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMP.dir/src/core/sequence.cpp.o -c /construction/biology/hyphy/hyphy-2.3.13/src/core/sequence.cpp --- CMakeFiles/HYPHYMP.dir/src/core/simplelist.cpp.o --- [ 65%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/simplelist.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHY_64__ -D__MP2__ -D__MP__ -D__UNIX__ -I/construction/biology/hyphy/hyphy-2.3.13/src/core/include -I/construction/biology/hyphy/hyphy-2.3.13/src/lib/Link -I/construction/biology/hyphy/hyphy-2.3.13/src/new/include -I/construction/biology/hyphy/hyphy-2.3.13/contrib/SQLite-3.8.2 -I/construction/biology/hyphy/hyphy-2.3.13/contrib/gtest-1.7.0/include -I/construction/biology/hyphy/hyphy-2.3.13/tests/gtests -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=gnu++14 -march=corei7-avx -mtune=corei7-avx -w -fopenmp -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMP.dir/src/core/simplelist.cpp.o -c /construction/biology/hyphy/hyphy-2.3.13/src/core/simplelist.cpp --- CMakeFiles/HYPHYMP.dir/src/core/site.cpp.o --- [ 68%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/site.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHY_64__ -D__MP2__ -D__MP__ -D__UNIX__ -I/construction/biology/hyphy/hyphy-2.3.13/src/core/include -I/construction/biology/hyphy/hyphy-2.3.13/src/lib/Link -I/construction/biology/hyphy/hyphy-2.3.13/src/new/include -I/construction/biology/hyphy/hyphy-2.3.13/contrib/SQLite-3.8.2 -I/construction/biology/hyphy/hyphy-2.3.13/contrib/gtest-1.7.0/include -I/construction/biology/hyphy/hyphy-2.3.13/tests/gtests -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=gnu++14 -march=corei7-avx -mtune=corei7-avx -w -fopenmp -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMP.dir/src/core/site.cpp.o -c /construction/biology/hyphy/hyphy-2.3.13/src/core/site.cpp --- CMakeFiles/HYPHYMP.dir/src/core/stack.cpp.o --- [ 68%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/stack.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHY_64__ -D__MP2__ -D__MP__ -D__UNIX__ -I/construction/biology/hyphy/hyphy-2.3.13/src/core/include -I/construction/biology/hyphy/hyphy-2.3.13/src/lib/Link -I/construction/biology/hyphy/hyphy-2.3.13/src/new/include -I/construction/biology/hyphy/hyphy-2.3.13/contrib/SQLite-3.8.2 -I/construction/biology/hyphy/hyphy-2.3.13/contrib/gtest-1.7.0/include -I/construction/biology/hyphy/hyphy-2.3.13/tests/gtests -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=gnu++14 -march=corei7-avx -mtune=corei7-avx -w -fopenmp -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMP.dir/src/core/stack.cpp.o -c /construction/biology/hyphy/hyphy-2.3.13/src/core/stack.cpp 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CMakeFiles/HYPHYMP.dir/src/core/string_file_wrapper.cpp.o -c /construction/biology/hyphy/hyphy-2.3.13/src/core/string_file_wrapper.cpp --- CMakeFiles/HYPHYMP.dir/src/core/strings.cpp.o --- [ 75%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/strings.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHY_64__ -D__MP2__ -D__MP__ -D__UNIX__ -I/construction/biology/hyphy/hyphy-2.3.13/src/core/include -I/construction/biology/hyphy/hyphy-2.3.13/src/lib/Link -I/construction/biology/hyphy/hyphy-2.3.13/src/new/include -I/construction/biology/hyphy/hyphy-2.3.13/contrib/SQLite-3.8.2 -I/construction/biology/hyphy/hyphy-2.3.13/contrib/gtest-1.7.0/include -I/construction/biology/hyphy/hyphy-2.3.13/tests/gtests -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 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/construction/biology/hyphy/stage/usr/local/lib/hyphy/TemplateBatchFiles/MEME_mf.bf -- Installing: /construction/biology/hyphy/stage/usr/local/lib/hyphy/TemplateBatchFiles/AnalyzeNucProtData.bf -- Installing: /construction/biology/hyphy/stage/usr/local/lib/hyphy/TemplateBatchFiles/TestCladeMeans.bf -- Installing: /construction/biology/hyphy/stage/usr/local/lib/hyphy/TemplateBatchFiles/Gateaux2.bf -- Installing: /construction/biology/hyphy/stage/usr/local/lib/hyphy/TemplateBatchFiles/BivariateCodonRateAnalysis.bf -- Installing: /construction/biology/hyphy/stage/usr/local/lib/hyphy/TemplateBatchFiles/post_npbs.bf -- Installing: /construction/biology/hyphy/stage/usr/local/bin/HYPHYMP ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for hyphy-2.3.13 file sizes/checksums [596]: ...... done packing files [596]: ...... done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 30 AUG 2018 at 13:04:11 UTC Duration: 00:02:26