------------------------------------------------------------------------------- -- 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-2.5.29: 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 00:00:01 ------------------------------------------------------------------------------- -- 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=600100 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-1.1.1k_1,1.txz Installing /packages/All/curl-7.76.0.txz Installing /packages/All/expat-2.2.10.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-6.2.20210313_1.txz ===== Message from ncurses-6.2.20210313_1: -- { type: install message: < hyphy-2.5.29 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> hyphy-2.5.29 depends on file: /usr/local/sbin/pkg - found => veg-hyphy-2.5.29_GH0.tar.gz doesn't seem to exist in /distfiles/. => Attempting to fetch https://codeload.github.com/veg/hyphy/tar.gz/2.5.29?dummy=/veg-hyphy-2.5.29_GH0.tar.gz fetch: https://codeload.github.com/veg/hyphy/tar.gz/2.5.29?dummy=/veg-hyphy-2.5.29_GH0.tar.gz: size unknown fetch: https://codeload.github.com/veg/hyphy/tar.gz/2.5.29?dummy=/veg-hyphy-2.5.29_GH0.tar.gz: size of remote file is not known veg-hyphy-2.5.29_GH0.tar.gz 0 B 0 Bps veg-hyphy-2.5.29_GH0.tar.gz 3840 kB 5402 kBps veg-hyphy-2.5.29_GH0.tar.gz 5216 kB 5066 kBps 01s ===> Fetching all distfiles required by hyphy-2.5.29 for building SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> hyphy-2.5.29 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by hyphy-2.5.29 for building => SHA256 Checksum OK for veg-hyphy-2.5.29_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> hyphy-2.5.29 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by hyphy-2.5.29 for building ===> Extracting for hyphy-2.5.29 => SHA256 Checksum OK for veg-hyphy-2.5.29_GH0.tar.gz. Extracted Memory Use: 28.78M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for hyphy-2.5.29 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> hyphy-2.5.29 depends on file: /usr/local/bin/cmake - found ===> hyphy-2.5.29 depends on file: /usr/local/lib/libcrypto.so.11 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> hyphy-2.5.29 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> hyphy-2.5.29 depends on file: /usr/local/bin/cmake - found ===> hyphy-2.5.29 depends on file: /usr/local/lib/libcrypto.so.11 - found ===> hyphy-2.5.29 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> Configuring for hyphy-2.5.29 ===> 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 "7.76.0") 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) Reason given by package: MPI component 'Fortran' was requested, but language Fortran is not enabled. -- 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 00:00:03 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for hyphy-2.5.29 /usr/local/bin/cmake -S/construction/biology/hyphy/hyphy-2.5.29 -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 /construction/biology/hyphy/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hyphy/hyphy-2.5.29 /construction/biology/hyphy/hyphy-2.5.29 /construction/biology/hyphy/.build /construction/biology/hyphy/.build /construction/biology/hyphy/.build/CMakeFiles/hyphy.dir/DependInfo.cmake Scanning dependencies of target hyphy /usr/bin/make -f CMakeFiles/hyphy.dir/build.make CMakeFiles/hyphy.dir/build --- CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o --- --- CMakeFiles/hyphy.dir/src/core/alignment.cpp.o --- --- CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o --- --- CMakeFiles/hyphy.dir/src/core/avllist.cpp.o --- --- CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o --- --- CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o --- --- CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o --- --- CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o --- --- CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o --- --- CMakeFiles/hyphy.dir/src/core/batchlan.cpp.o --- --- CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o --- [ 3%] Building CXX object CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.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__ -I/construction/biology/hyphy/hyphy-2.5.29/src/core/include -I/construction/biology/hyphy/hyphy-2.5.29/src/contrib -I/construction/biology/hyphy/hyphy-2.5.29/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.29/src/new/include -I/construction/biology/hyphy/hyphy-2.5.29/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 -o CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -c /construction/biology/hyphy/hyphy-2.5.29/src/core/_hyExecutionContext.cpp --- CMakeFiles/hyphy.dir/src/core/alignment.cpp.o --- [ 3%] Building CXX object 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__ -I/construction/biology/hyphy/hyphy-2.5.29/src/core/include -I/construction/biology/hyphy/hyphy-2.5.29/src/contrib -I/construction/biology/hyphy/hyphy-2.5.29/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.29/src/new/include -I/construction/biology/hyphy/hyphy-2.5.29/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 -o CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -c /construction/biology/hyphy/hyphy-2.5.29/src/core/alignment.cpp --- CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o --- [ 3%] Building CXX object CMakeFiles/hyphy.dir/src/core/associative_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__ -I/construction/biology/hyphy/hyphy-2.5.29/src/core/include -I/construction/biology/hyphy/hyphy-2.5.29/src/contrib -I/construction/biology/hyphy/hyphy-2.5.29/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.29/src/new/include -I/construction/biology/hyphy/hyphy-2.5.29/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 -o CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -c /construction/biology/hyphy/hyphy-2.5.29/src/core/associative_list.cpp --- CMakeFiles/hyphy.dir/src/core/avllist.cpp.o --- [ 7%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllist.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__ -I/construction/biology/hyphy/hyphy-2.5.29/src/core/include -I/construction/biology/hyphy/hyphy-2.5.29/src/contrib -I/construction/biology/hyphy/hyphy-2.5.29/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.29/src/new/include -I/construction/biology/hyphy/hyphy-2.5.29/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 -o CMakeFiles/hyphy.dir/src/core/avllist.cpp.o -c /construction/biology/hyphy/hyphy-2.5.29/src/core/avllist.cpp --- CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o --- [ 7%] Building CXX object 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__ -D__MP2__ -D__MP__ -D__UNIX__ -I/construction/biology/hyphy/hyphy-2.5.29/src/core/include -I/construction/biology/hyphy/hyphy-2.5.29/src/contrib -I/construction/biology/hyphy/hyphy-2.5.29/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.29/src/new/include -I/construction/biology/hyphy/hyphy-2.5.29/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 -o CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o -c /construction/biology/hyphy/hyphy-2.5.29/src/core/avllistx.cpp --- CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o --- [ 11%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx_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__ -I/construction/biology/hyphy/hyphy-2.5.29/src/core/include -I/construction/biology/hyphy/hyphy-2.5.29/src/contrib -I/construction/biology/hyphy/hyphy-2.5.29/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.29/src/new/include -I/construction/biology/hyphy/hyphy-2.5.29/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 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-I/construction/biology/hyphy/hyphy-2.5.29/src/new/include -I/construction/biology/hyphy/hyphy-2.5.29/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 -o CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o -c /construction/biology/hyphy/hyphy-2.5.29/src/core/fisher_exact.cpp --- CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o --- [ 30%] 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__ -I/construction/biology/hyphy/hyphy-2.5.29/src/core/include -I/construction/biology/hyphy/hyphy-2.5.29/src/contrib -I/construction/biology/hyphy/hyphy-2.5.29/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.29/src/new/include -I/construction/biology/hyphy/hyphy-2.5.29/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 -o CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o -c /construction/biology/hyphy/hyphy-2.5.29/src/core/dataset_filter_numeric.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__ -I/construction/biology/hyphy/hyphy-2.5.29/src/core/include 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-I/construction/biology/hyphy/hyphy-2.5.29/src/core/include -I/construction/biology/hyphy/hyphy-2.5.29/src/contrib -I/construction/biology/hyphy/hyphy-2.5.29/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.29/src/new/include -I/construction/biology/hyphy/hyphy-2.5.29/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 -o CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o -c /construction/biology/hyphy/hyphy-2.5.29/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__ 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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__ -I/construction/biology/hyphy/hyphy-2.5.29/src/core/include -I/construction/biology/hyphy/hyphy-2.5.29/src/contrib -I/construction/biology/hyphy/hyphy-2.5.29/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.29/src/new/include -I/construction/biology/hyphy/hyphy-2.5.29/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 -o CMakeFiles/hyphy.dir/src/core/operation.cpp.o -c /construction/biology/hyphy/hyphy-2.5.29/src/core/operation.cpp --- 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__ -I/construction/biology/hyphy/hyphy-2.5.29/src/core/include -I/construction/biology/hyphy/hyphy-2.5.29/src/contrib -I/construction/biology/hyphy/hyphy-2.5.29/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.29/src/new/include -I/construction/biology/hyphy/hyphy-2.5.29/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 -o CMakeFiles/hyphy.dir/src/core/parser.cpp.o -c /construction/biology/hyphy/hyphy-2.5.29/src/core/parser.cpp --- CMakeFiles/hyphy.dir/src/core/parser2.cpp.o --- [ 53%] Building CXX object 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__ -I/construction/biology/hyphy/hyphy-2.5.29/src/core/include -I/construction/biology/hyphy/hyphy-2.5.29/src/contrib -I/construction/biology/hyphy/hyphy-2.5.29/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.29/src/new/include -I/construction/biology/hyphy/hyphy-2.5.29/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 -o CMakeFiles/hyphy.dir/src/core/parser2.cpp.o -c /construction/biology/hyphy/hyphy-2.5.29/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__ -I/construction/biology/hyphy/hyphy-2.5.29/src/core/include -I/construction/biology/hyphy/hyphy-2.5.29/src/contrib -I/construction/biology/hyphy/hyphy-2.5.29/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.29/src/new/include -I/construction/biology/hyphy/hyphy-2.5.29/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 -o CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o -c /construction/biology/hyphy/hyphy-2.5.29/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__ -I/construction/biology/hyphy/hyphy-2.5.29/src/core/include -I/construction/biology/hyphy/hyphy-2.5.29/src/contrib -I/construction/biology/hyphy/hyphy-2.5.29/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.29/src/new/include -I/construction/biology/hyphy/hyphy-2.5.29/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 -o CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o -c /construction/biology/hyphy/hyphy-2.5.29/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__ -I/construction/biology/hyphy/hyphy-2.5.29/src/core/include -I/construction/biology/hyphy/hyphy-2.5.29/src/contrib -I/construction/biology/hyphy/hyphy-2.5.29/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.29/src/new/include -I/construction/biology/hyphy/hyphy-2.5.29/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 -o CMakeFiles/hyphy.dir/src/core/site.cpp.o -c /construction/biology/hyphy/hyphy-2.5.29/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__ -I/construction/biology/hyphy/hyphy-2.5.29/src/core/include -I/construction/biology/hyphy/hyphy-2.5.29/src/contrib -I/construction/biology/hyphy/hyphy-2.5.29/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.29/src/new/include -I/construction/biology/hyphy/hyphy-2.5.29/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 -o CMakeFiles/hyphy.dir/src/core/stack.cpp.o -c /construction/biology/hyphy/hyphy-2.5.29/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__ -I/construction/biology/hyphy/hyphy-2.5.29/src/core/include -I/construction/biology/hyphy/hyphy-2.5.29/src/contrib -I/construction/biology/hyphy/hyphy-2.5.29/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.29/src/new/include -I/construction/biology/hyphy/hyphy-2.5.29/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 -o CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o -c /construction/biology/hyphy/hyphy-2.5.29/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__ -I/construction/biology/hyphy/hyphy-2.5.29/src/core/include -I/construction/biology/hyphy/hyphy-2.5.29/src/contrib -I/construction/biology/hyphy/hyphy-2.5.29/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.29/src/new/include -I/construction/biology/hyphy/hyphy-2.5.29/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 -o CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o -c /construction/biology/hyphy/hyphy-2.5.29/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__ -I/construction/biology/hyphy/hyphy-2.5.29/src/core/include -I/construction/biology/hyphy/hyphy-2.5.29/src/contrib -I/construction/biology/hyphy/hyphy-2.5.29/src/lib/Link -I/construction/biology/hyphy/hyphy-2.5.29/src/new/include -I/construction/biology/hyphy/hyphy-2.5.29/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 -o 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/construction/biology/hyphy/stage/usr/local/share/hyphy/TemplateBatchFiles/partitionSequences.ibf -- Installing: /construction/biology/hyphy/stage/usr/local/share/hyphy/TemplateBatchFiles/posteriors.ibf -- Installing: /construction/biology/hyphy/stage/usr/local/share/hyphy/TemplateBatchFiles/qndhelper1.ibf -- Installing: /construction/biology/hyphy/stage/usr/local/share/hyphy/TemplateBatchFiles/qndhelper1_mf.ibf -- Installing: /construction/biology/hyphy/stage/usr/local/share/hyphy/TemplateBatchFiles/qndhelper2.ibf -- Installing: /construction/biology/hyphy/stage/usr/local/share/hyphy/TemplateBatchFiles/qndhelper2_mf.ibf -- Installing: /construction/biology/hyphy/stage/usr/local/share/hyphy/TemplateBatchFiles/qndhelper3.ibf -- Installing: /construction/biology/hyphy/stage/usr/local/share/hyphy/TemplateBatchFiles/qndhelper4.ibf -- Installing: /construction/biology/hyphy/stage/usr/local/share/hyphy/TemplateBatchFiles/queryTree.bf -- Installing: /construction/biology/hyphy/stage/usr/local/share/hyphy/TemplateBatchFiles/readIndexFile.bf -- Installing: /construction/biology/hyphy/stage/usr/local/share/hyphy/TemplateBatchFiles/relative_nucleotide_rates.bf -- Installing: /construction/biology/hyphy/stage/usr/local/share/hyphy/TemplateBatchFiles/relrateBootstrap.bf -- Installing: /construction/biology/hyphy/stage/usr/local/share/hyphy/TemplateBatchFiles/relratioBootstrap.bf -- Installing: /construction/biology/hyphy/stage/usr/local/share/hyphy/TemplateBatchFiles/selectModelParameters.bf -- Installing: /construction/biology/hyphy/stage/usr/local/share/hyphy/TemplateBatchFiles/simpleBootstrap.bf -- Installing: /construction/biology/hyphy/stage/usr/local/share/hyphy/data -- Installing: /construction/biology/hyphy/stage/usr/local/share/hyphy/data/.DS_Store -- Installing: /construction/biology/hyphy/stage/usr/local/share/hyphy/data/brown.nuc -- Installing: /construction/biology/hyphy/stage/usr/local/share/hyphy/data/integrase_BDA.nex -- Installing: /construction/biology/hyphy/stage/usr/local/share/hyphy/data/p51.aa -- Installing: /construction/biology/hyphy/stage/usr/local/share/hyphy/data/p51.nex -- Installing: /construction/biology/hyphy/stage/usr/local/bin/hyphy ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:03 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for hyphy-2.5.29 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 00:00:16 TOTAL TIME 00:04:46