=>> Building biology/hyphy build started at Tue Dec 16 06:30:29 EST 2025 port directory: /usr/ports/biology/hyphy package name: hyphy-2.5.88 building for: FreeBSD pkg.DaveG.ca 14.3-RELEASE-p1 FreeBSD 14.3-RELEASE-p1 1403000 amd64 maintained by: jrm@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1100 Dec 13 21:11 /usr/ports/biology/hyphy/Makefile Ports top last git commit: 10f7dee57a4c Ports top unclean checkout: no Port dir last git commit: 02998ed5b496 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1403000 Job Id: 02 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1403000 UNAME_v=FreeBSD 14.3-RELEASE-p1 1403000 UNAME_r=14.3-RELEASE-p1 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_14_3_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_14_3_x64-HEAD-ALL/02/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_3_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_3_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for hyphy-2.5.88: AVX=off: Support for AVX (Advanced Vector Extensions) instructions FMA3=off: Support for FMA3 (Fused Multiply-Add) instructions on x86 NEON=off: Support for NEON SIMD instructions on ARM SSE4=off: Support for SSE4 (Streaming SIMD Extensions) instructions TARGET_NATIVE=off: Enable CPU-specific optimizations for the build machine ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- jrm@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/hyphy/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/hyphy/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/hyphy/work/.cache HOME=/wrkdirs/usr/ports/biology/hyphy/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/hyphy/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/hyphy/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/hyphy/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/hyphy/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/hyphy/work/.cache HOME=/wrkdirs/usr/ports/biology/hyphy/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/hyphy/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/hyphy/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DESTDIR=/wrkdirs/usr/ports/biology/hyphy/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- CMAKE_BUILD_TYPE="release" OSREL=14.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/hyphy" EXAMPLESDIR="share/examples/hyphy" DATADIR="share/hyphy" WWWDIR="www/hyphy" ETCDIR="etc/hyphy" --End PLIST_SUB-- --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 --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> hyphy-2.5.88 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.4.2_1.pkg [pkg.DaveG.ca] Installing pkg-2.4.2_1... [pkg.DaveG.ca] Extracting pkg-2.4.2_1: .......... done ===> hyphy-2.5.88 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of hyphy-2.5.88 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 => veg-hyphy-2.5.88_GH0.tar.gz doesn't seem to exist in /portdistfiles. => Attempting to fetch https://codeload.github.com/veg/hyphy/tar.gz/2.5.88?dummy=/veg-hyphy-2.5.88_GH0.tar.gz fetch: https://codeload.github.com/veg/hyphy/tar.gz/2.5.88?dummy=/veg-hyphy-2.5.88_GH0.tar.gz: size unknown fetch: https://codeload.github.com/veg/hyphy/tar.gz/2.5.88?dummy=/veg-hyphy-2.5.88_GH0.tar.gz: size of remote file is not known veg-hyphy-2.5.88_GH0.tar.gz 4270 kB 850 kBps 05s ===> Fetching all distfiles required by hyphy-2.5.88 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by hyphy-2.5.88 for building => SHA256 Checksum OK for veg-hyphy-2.5.88_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by hyphy-2.5.88 for building ===> Extracting for hyphy-2.5.88 => SHA256 Checksum OK for veg-hyphy-2.5.88_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for hyphy-2.5.88 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> hyphy-2.5.88 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.10.pkg [pkg.DaveG.ca] Installing cmake-core-3.31.10... [pkg.DaveG.ca] `-- Installing expat-2.7.3... [pkg.DaveG.ca] `-- Extracting expat-2.7.3: .......... done [pkg.DaveG.ca] `-- Installing jsoncpp-1.9.6_1... [pkg.DaveG.ca] `-- Extracting jsoncpp-1.9.6_1: .......... done [pkg.DaveG.ca] `-- Installing libidn2-2.3.8... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | `-- Installing libunistring-1.4.1... [pkg.DaveG.ca] | `-- Extracting libunistring-1.4.1: .......... done [pkg.DaveG.ca] `-- Extracting libidn2-2.3.8: .......... done [pkg.DaveG.ca] `-- Installing libuv-1.51.0... [pkg.DaveG.ca] `-- Extracting libuv-1.51.0: .......... done [pkg.DaveG.ca] `-- Installing rhash-1.4.4_2... [pkg.DaveG.ca] | `-- Installing gettext-runtime-0.23.1... [pkg.DaveG.ca] | `-- Extracting gettext-runtime-0.23.1: .......... done [pkg.DaveG.ca] `-- Extracting rhash-1.4.4_2: .......... done [pkg.DaveG.ca] Extracting cmake-core-3.31.10: .......... done ===> hyphy-2.5.88 depends on file: /usr/local/bin/cmake - found ===> Returning to build of hyphy-2.5.88 ===> hyphy-2.5.88 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.13.1,4.pkg [pkg.DaveG.ca] Installing ninja-1.13.1,4... [pkg.DaveG.ca] `-- Installing python311-3.11.14... [pkg.DaveG.ca] | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | `-- Installing readline-8.3.1... [pkg.DaveG.ca] | `-- Extracting readline-8.3.1: .......... done [pkg.DaveG.ca] `-- Extracting python311-3.11.14: .......... done [pkg.DaveG.ca] Extracting ninja-1.13.1,4: ..... done ===== Message from python311-3.11.14: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> hyphy-2.5.88 depends on executable: ninja - found ===> Returning to build of hyphy-2.5.88 ===> hyphy-2.5.88 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> hyphy-2.5.88 depends on file: /usr/local/bin/ccache - found ===> Returning to build of hyphy-2.5.88 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> hyphy-2.5.88 depends on shared library: libcurl.so - not found ===> Installing existing package /packages/All/curl-8.17.0.pkg [pkg.DaveG.ca] Installing curl-8.17.0... [pkg.DaveG.ca] `-- Installing brotli-1.2.0,1... [pkg.DaveG.ca] `-- Extracting brotli-1.2.0,1: .......... done [pkg.DaveG.ca] `-- Installing libnghttp2-1.68.0... [pkg.DaveG.ca] `-- Extracting libnghttp2-1.68.0: ....... done [pkg.DaveG.ca] `-- Installing libpsl-0.21.5_2... [pkg.DaveG.ca] `-- Extracting libpsl-0.21.5_2: ........ done [pkg.DaveG.ca] `-- Installing libssh2-1.11.1,3... [pkg.DaveG.ca] `-- Extracting libssh2-1.11.1,3: .......... done [pkg.DaveG.ca] `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] Extracting curl-8.17.0: .......... done ===> hyphy-2.5.88 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> Returning to build of hyphy-2.5.88 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for hyphy-2.5.88 ===> Performing in-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88 -- The CXX compiler identification is Clang 19.1.7 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HYPHY_HAVE_SVE -- Performing Test HYPHY_HAVE_SVE - Failed -- Found OpenMP_CXX: -fopenmp=libomp (found version "5.1") -- Found OpenMP: TRUE (found version "5.1") -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Could NOT find BLAS (missing: BLAS_LIBRARIES) -- Found CURL: /usr/local/lib/libcurl.so (found version "8.17.0") -- Found ZLIB: /usr/lib/libz.so (found version "1.3.1") -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_CXX_FOUND) -- Configuring done (17.1s) -- Generating done (0.3s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_COLOR_MAKEFILE CMAKE_C_COMPILER CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE FETCHCONTENT_FULLY_DISCONNECTED NOFMA3 -- Build files have been written to: /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for hyphy-2.5.88 [ 1% 64/67] /usr/local/libexec/ccache/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/new/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -mno-sse3 -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -MF CMakeFiles/hyphy.dir/src/core/alignment.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/alignment.cpp [ 2% 65/67] /usr/local/libexec/ccache/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/new/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -mno-sse3 -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -fopenmp=libomp -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 /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/avllist.cpp [ 4% 66/67] /usr/local/libexec/ccache/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/new/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -mno-sse3 -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -fopenmp=libomp -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 /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/avllistx_iterator.cpp [ 5% 66/67] /usr/local/libexec/ccache/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/new/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -mno-sse3 -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o -MF CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/avllistxl_iterator.cpp [ 7% 66/67] /usr/local/libexec/ccache/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/lib/Link 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-I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/new/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -mno-sse3 -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o -MF CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/variablecontainer.cpp [ 79% 66/67] /usr/local/libexec/ccache/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/new/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -mno-sse3 -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -fopenmp=libomp -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 /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/trie_iterator.cpp [ 80% 66/67] /usr/local/libexec/ccache/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/new/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -mno-sse3 -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -fopenmp=libomp -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 /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/polynoml.cpp [ 82% 66/67] /usr/local/libexec/ccache/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/new/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -mno-sse3 -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o -MF CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o.d -o CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/new/bayesgraph.cpp [ 83% 66/67] /usr/local/libexec/ccache/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/new/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -mno-sse3 -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -fopenmp=libomp -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 /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/simplelist.cpp [ 85% 66/67] /usr/local/libexec/ccache/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/new/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -mno-sse3 -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -fopenmp=libomp -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 /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/tree_evaluator.cpp /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/tree_evaluator.cpp:639:6: warning: loop not unrolled: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] 639 | void _hy_matrix_vector_product_blocked_4x4(double *C, double const *M, | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/tree_evaluator.cpp:639:6: warning: loop not unrolled: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/tree_evaluator.cpp:639:6: warning: loop not unrolled: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/tree_evaluator.cpp:639:6: warning: loop not unrolled: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] 4 warnings generated. [ 86% 66/67] /usr/local/libexec/ccache/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/new/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -mno-sse3 -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o -MF CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o.d -o CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/new/bayesgraph2.cpp [ 88% 66/67] /usr/local/libexec/ccache/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/new/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -mno-sse3 -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/mains/unix.cpp.o -MF CMakeFiles/hyphy.dir/src/mains/unix.cpp.o.d -o CMakeFiles/hyphy.dir/src/mains/unix.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/mains/unix.cpp [ 89% 66/67] /usr/local/libexec/ccache/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/new/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -mno-sse3 -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -fopenmp=libomp -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 /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/topology.cpp [ 91% 66/67] /usr/local/libexec/ccache/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/new/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -mno-sse3 -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -fopenmp=libomp -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 /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/batchlanruntime.cpp [ 92% 66/67] /usr/local/libexec/ccache/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/new/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -mno-sse3 -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/new/scfg.cpp.o -MF CMakeFiles/hyphy.dir/src/new/scfg.cpp.o.d -o CMakeFiles/hyphy.dir/src/new/scfg.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/new/scfg.cpp [ 94% 66/67] /usr/local/libexec/ccache/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/new/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -mno-sse3 -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -fopenmp=libomp -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 /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/tree.cpp [ 95% 66/67] /usr/local/libexec/ccache/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/new/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -mno-sse3 -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -fopenmp=libomp -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 /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/strings.cpp /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/strings.cpp:134:35: warning: format string is not a string literal [-Wformat-nonliteral] 134 | s_length = snprintf(s_val, 128, format ? format : PRINTF_FORMAT_STRING, val); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1 warning generated. [ 97% 66/67] /usr/local/libexec/ccache/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/new/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -mno-sse3 -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -fopenmp=libomp -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 /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/likefunc.cpp /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/likefunc.cpp:5964:72: warning: unused parameter 'sig_term' [-Wunused-parameter] 5964 | void _LikelihoodFunction::_TerminateAndDump(const _String &error, bool sig_term, | ^ 1 warning generated. [ 98% 66/67] /usr/local/libexec/ccache/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/new/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -mno-sse3 -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -fopenmp=libomp -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 /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/matrix.cpp /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/matrix.cpp:4346:36: warning: declaration shadows a local variable [-Wshadow] 4346 | for (unsigned long i = 0UL; i < 60UL; i += 4UL) { | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/matrix.cpp:4291:22: note: previous declaration is here 4291 | long i = ((unsigned long)m) % 61; | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/matrix.cpp:5480:15: warning: loop not unrolled: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] 5480 | void _Matrix::CopyMatrixToDenseAndMultiply(_Matrix const &source, hyFloat C, | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.88/src/core/matrix.cpp:5480:15: warning: loop not unrolled: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning] 3 warnings generated. [100% 67/67] : && /usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -L/usr/local/lib -Xlinker --dependency-file=CMakeFiles/hyphy.dir/link.d 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/batchlan2.cpp.o CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o 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/wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA_empirical.mdl -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/CF3x4.bf -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/S4 -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/defineGamma.mdl -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/MG94customFreqs.mdl -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/GRM.mdl -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/mtMAM.mdl -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/binomial.ibf -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/SingleBreakpointRecomb.bf -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/KHTest.bf -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/WANC.bf -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/data -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/data/p51.nex -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/data/p51.aa -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/data/integrase_BDA.nex -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/data/brown.nuc -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/README.md -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/bin/hyphy ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-12-16T11:30:29+0000' 'PKG_NOTE_ports_top_git_hash=10f7dee57a4c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=02998ed5b496' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for hyphy-2.5.88 ===> Building hyphy-2.5.88 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for hyphy-2.5.88 build of biology/hyphy | hyphy-2.5.88 ended at Tue Dec 16 06:32:01 EST 2025 build time: 00:01:36