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Maintainer: [email protected] Log URL: https://pkg-status.freebsd.org/beefy21/data/142i386-default/645916cd07f7/logs/hyphy-2.5.77_1.log Build URL: https://pkg-status.freebsd.org/beefy21/build.html?mastername=142i386-default&build=645916cd07f7 Log: =>> Building biology/hyphy build started at Thu Aug 21 01:10:22 UTC 2025 port directory: /usr/ports/biology/hyphy package name: hyphy-2.5.77_1 building for: FreeBSD 142i386-default-job-33 14.2-RELEASE-p5 FreeBSD 14.2-RELEASE-p5 i386 maintained by: [email protected] Makefile datestamp: -rw-r--r-- 1 root wheel 803 Aug 19 01:01 /usr/ports/biology/hyphy/Makefile Ports top last git commit: 645916cd07 Ports top unclean checkout: no Port dir last git commit: 856ecd7543 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.3 Host OSVERSION: 1500052 Jail OSVERSION: 1402000 Job Id: 33 ---Begin Environment--- SHELL=/bin/sh BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 OSVERSION=1402000 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 UNAME_m=i386 UNAME_p=i386 UNAME_r=14.2-RELEASE-p5 LOCALBASE=/usr/local UNAME_v=FreeBSD 14.2-RELEASE-p5 USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.3 MASTERMNT=/usr/local/poudriere/data/.m/142i386-default/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/142i386-default/33/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=142i386-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/142i386-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.3 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-2.5.77_1: AVX=off: Advanced vector extensions support TARGET_NATIVE=off: Enable CPU-specific instructions and tuning for build machine ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- [email protected] --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/lo cal/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=14.2 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--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=i386 MACHINE_ARCH=i386 ARCH=${MACHINE_ARCH} #### #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs MAKE_JOBS_NUMBER=3 #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 524288 stack size (kbytes, -s) 65536 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-- =======================<phase: check-sanity >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> hyphy-2.5.77_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.2.2.pkg [142i386-default-job-33] Installing pkg-2.2.2... [142i386-default-job-33] Extracting pkg-2.2.2: .......... done ===> hyphy-2.5.77_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of hyphy-2.5.77_1 =========================================================================== =======================<phase: fetch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: fetch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user ===> Fetching all distfiles required by hyphy-2.5.77_1 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user ===> Fetching all distfiles required by hyphy-2.5.77_1 for building => SHA256 Checksum OK for veg-hyphy-2.5.77_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: extract >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user ===> Fetching all distfiles required by hyphy-2.5.77_1 for building ===> Extracting for hyphy-2.5.77_1 => SHA256 Checksum OK for veg-hyphy-2.5.77_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: patch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for hyphy-2.5.77_1 =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> hyphy-2.5.77_1 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.7.pkg [142i386-default-job-33] Installing cmake-core-3.31.7... [142i386-default-job-33] `-- Installing expat-2.7.1... [142i386-default-job-33] `-- Extracting expat-2.7.1: .......... done [142i386-default-job-33] `-- Installing jsoncpp-1.9.6_1... [142i386-default-job-33] `-- Extracting jsoncpp-1.9.6_1: .......... done [142i386-default-job-33] `-- Installing libidn2-2.3.8... [142i386-default-job-33] | `-- Installing indexinfo-0.3.1_1... [142i386-default-job-33] | `-- Extracting indexinfo-0.3.1_1: .... done [142i386-default-job-33] | `-- Installing libunistring-1.3... [142i386-default-job-33] | `-- Extracting libunistring-1.3: .......... done [142i386-default-job-33] `-- Extracting libidn2-2.3.8: .......... done [142i386-default-job-33] `-- Installing libuv-1.51.0... [142i386-default-job-33] `-- Extracting libuv-1.51.0: .......... done [142i386-default-job-33] `-- Installing rhash-1.4.4_1... <snip> py311-tkinter x11-toolkits/py-tkinter@py311 ===> hyphy-2.5.77_1 depends on executable: ninja - found ===> Returning to build of hyphy-2.5.77_1 =========================================================================== =======================<phase: lib-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> hyphy-2.5.77_1 depends on shared library: libcurl.so - not found ===> Installing existing package /packages/All/curl-8.15.0.pkg [142i386-default-job-33] Installing curl-8.15.0... [142i386-default-job-33] `-- Installing brotli-1.1.0,1... [142i386-default-job-33] `-- Extracting brotli-1.1.0,1: .......... done [142i386-default-job-33] `-- Installing libnghttp2-1.66.0... [142i386-default-job-33] `-- Extracting libnghttp2-1.66.0: .......... done [142i386-default-job-33] `-- Installing libpsl-0.21.5_2... [142i386-default-job-33] `-- Extracting libpsl-0.21.5_2: .......... done [142i386-default-job-33] `-- Installing libssh2-1.11.1,3... [142i386-default-job-33] `-- Extracting libssh2-1.11.1,3: .......... done [142i386-default-job-33] `-- Installing zstd-1.5.7... [142i386-default-job-33] | `-- Installing liblz4-1.10.0,1... [142i386-default-job-33] | `-- Extracting liblz4-1.10.0,1: .......... done [142i386-default-job-33] `-- Extracting zstd-1.5.7: .......... done [142i386-default-job-33] Extracting curl-8.15.0: .......... done ===> hyphy-2.5.77_1 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> Returning to build of hyphy-2.5.77_1 =========================================================================== =======================<phase: configure >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for hyphy-2.5.77_1 ===> Performing in-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77 -- The CXX compiler identification is Clang 18.1.6 -- 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 HYPHY_HAVE_NEON -- Performing Test HYPHY_HAVE_NEON - Failed -- Performing Test HYPHY_HAVE_SSE41 -- Performing Test HYPHY_HAVE_SSE41 - Success -- 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 "8.15.0") -- 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 (1.2s) -- Generating done (0.0s) 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 -- Build files have been written to: /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77 =========================================================================== =======================<phase: build >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for hyphy-2.5.77_1 [ 1% 1/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/new/include -O2 -pipe 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-D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/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++14 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -msse4.1 -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/p orts/biology/hyphy/work/hyphy-2.5.77/src/core/avllist.cpp [ 7% 5/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/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++14 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -msse4.1 -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o -MF CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o -c /wrkdirs/us r/ports/biology/hyphy/work/hyphy-2.5.77/src/core/avllistx.cpp [ 9% 6/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" 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CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o -c /wrkdirs /usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/avllistxl.cpp [ 12% 8/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/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++14 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -msse4.1 -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-2.5.77/src/core/avllistxl_iterator.cpp [ 13% 9/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/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++14 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 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-std=c++14 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -msse4.1 -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/core/batchlan.cpp.o -MF CMakeFiles/hyphy.dir/src/core/batchlan.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/batchlan.cpp.o -c /wrkdirs/u sr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/batchlan.cpp [ 16% 11/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/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++14 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -msse4.1 -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o -MF CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o -c /wrkdir s/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/batchlan2.cpp [ 18% 12/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/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++14 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -msse4.1 -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o -MF CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/batchlanhelper s.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/batchlanhelpers.cpp [ 19% 13/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/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++14 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -msse4.1 -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/batchlanruntim e.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/batchlanruntime.cpp /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/batchlanruntime.cpp:656:17: warning: compound literals are a C99-specific feature [-Wc99-extensions] 656 | (_associative_list_key_value){ | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/batchlanruntime.cpp:659:17: warning: compound literals are a C99-specific feature [-Wc99-extensions] 659 | (_associative_list_key_value){ | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/batchlanruntime.cpp:662:17: warning: compound literals are a C99-specific feature [-Wc99-extensions] 662 | (_associative_list_key_value){ | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/batchlanruntime.cpp:666:17: warning: compound literals are a C99-specific feature [-Wc99-extensions] 666 | (_associative_list_key_value){ | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/batchlanruntime.cpp:3975:28: warning: compound literals are a C99-specific feature [-Wc99-extensions] 3975 | (*kwargs) << (_associative_list_key_value){*my_key, my_object}; | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/batchlanruntime.cpp:3998:27: warning: compound literals are a C99-specific feature [-Wc99-extensions] 3998 | (*kwargs) < (_associative_list_key_value){_String(count), | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/batchlanruntime.cpp:4027:19: warning: compound literals are a C99-specific feature [-Wc99-extensions] 4027 | (_associative_list_key_value){"ID", | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/batchlanruntime.cpp:4029:19: warning: compound literals are a C99-specific feature [-Wc99-extensions] 4029 | (_associative_list_key_value){ | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/batchlanruntime.cpp:4108:13: warning: compound literals are a C99-specific feature [-Wc99-extensions] 4108 | (_associative_list_key_value){ | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/batchlanruntime.cpp:4111:13: warning: compound literals are a C99-specific feature [-Wc99-extensions] 4111 | (_associative_list_key_value){ | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/batchlanruntime.cpp:4114:13: warning: compound literals are a C99-specific feature [-Wc99-extensions] 4114 | (_associative_list_key_value){ | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/batchlanruntime.cpp:4207:21: warning: compound literals are a C99-specific feature [-Wc99-extensions] 4207 | (_associative_list_key_value){ | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/batchlanruntime.cpp:4209:21: warning: compound literals are a C99-specific feature [-Wc99-extensions] 4209 | (_associative_list_key_value){ | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/batchlanruntime.cpp:4211:21: warning: compound literals are a C99-specific feature [-Wc99-extensions] 4211 | (_associative_list_key_value){"MULT_BY_FREQ", | ^ 14 warnings generated. [ 21% 14/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/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++14 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -msse4.1 -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o -MF CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o -c /wrkdirs/u sr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/calcnode.cpp [ 22% 15/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/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++14 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -msse4.1 -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/core/category.cpp.o -MF CMakeFiles/hyphy.dir/src/core/category.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/category.cpp.o -c /wrkdirs/u sr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/category.cpp [ 24% 16/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/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++14 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -msse4.1 -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/core/constant.cpp.o -MF CMakeFiles/hyphy.dir/src/core/constant.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/constant.cpp.o -c /wrkdirs/u sr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/constant.cpp /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/constant.cpp:629:27: warning: format string is not a string literal [-Wformat-nonliteral] 629 | snprintf(buffer, 256, format, Value()); | ^~~~~~ 1 warning generated. [ 25% 17/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/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++14 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -msse4.1 -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/core/dataset.cpp.o -MF CMakeFiles/hyphy.dir/src/core/dataset.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/dataset.cpp.o -c /wrkdirs/usr/ ports/biology/hyphy/work/hyphy-2.5.77/src/core/dataset.cpp [ 27% 18/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/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++14 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -msse4.1 -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o -MF CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/dataset_filter.c pp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/dataset_filter.cpp [ 28% 19/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/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++14 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -msse4.1 -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o -MF CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/ dataset_filter_numeric.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/dataset_filter_numeric.cpp [ 30% 20/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/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++14 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -msse4.1 -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o -MF CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o - c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/fisher_exact.cpp [ 31% 21/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/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++14 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -msse4.1 -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/core/formula.cpp.o -MF CMakeFiles/hyphy.dir/src/core/formula.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/formula.cpp.o -c /wrkdirs/usr/ ports/biology/hyphy/work/hyphy-2.5.77/src/core/formula.cpp /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/formula.cpp:1285:40: warning: comparison of integers of different signs: 'unsigned int' and 'long' [-Wsign-compare] 1285 | for (unsigned int k = 2UL; k <= node_op_count; k++) { | ~ ^ ~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/formula.cpp:1296:38: warning: comparison of integers of different signs: 'unsigned int' and 'long' [-Wsign-compare] 1296 | for (unsigned int k = 2; k <= node_op_count; k++) { | ~ ^ ~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/formula.cpp:1318:35: warning: comparison of integers of different signs: 'unsigned int' and 'long' [-Wsign-compare] 1318 | for (unsigned int k = 2L; k <= argument_count; k++) { | ~ ^ ~~~~~~~~~~~~~~ 3 warnings generated. [ 33% 22/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/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++14 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -msse4.1 -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o -MF CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o.d -o CMakeFiles/hyphy.dir/src/cor e/formula_parsing_context.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/formula_parsing_context.cpp [ 34% 23/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/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++14 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -msse4.1 -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/core/fstring.cpp.o -MF CMakeFiles/hyphy.dir/src/core/fstring.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/fstring.cpp.o -c /wrkdirs/usr/ ports/biology/hyphy/work/hyphy-2.5.77/src/core/fstring.cpp [ 36% 24/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/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++14 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -msse4.1 -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o -MF CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/global _object_lists.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/global_object_lists.cpp [ 37% 25/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/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++14 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -msse4.1 -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/core/global_things.cpp.o -MF CMakeFiles/hyphy.dir/src/core/global_things.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/global_things.cpp. o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/global_things.cpp FAILED: CMakeFiles/hyphy.dir/src/core/global_things.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/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++14 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -Wshadow -Wformat=2 -Wunused -Wmost -msse4.1 -fopenmp=libomp -MD -MT CMakeFiles/hyphy.dir/src/core/global_things.cpp.o -MF CMakeFiles/hyphy.dir/src/core/global_things.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/global_things.cpp.o -c /wrkdirs /usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/global_things.cpp /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/global_things.cpp:176:62: error: conversion from 'size_t' (aka 'unsigned int') to 'const _String' is ambiguous 176 | HandleApplicationError(_String("Failed to allocate '") & bytes & "' bytes'", | ^~~~~ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include/hy_strings.h:127:3: note: candidate constructor 127 | _String(long const number); | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include/hy_strings.h:140:3: note: candidate constructor 140 | _String(const unsigned long sL, char *buffer = nil); | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include/hy_strings.h:151:3: note: candidate constructor 151 | _String(const hyFloat number, const char *format = nil); | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include/hy_strings.h:245:3: note: candidate constructor 245 | _String(const char c); | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/global_things.cpp:189:51: error: conversion from 'size_t' (aka 'unsigned int') to 'const _String' is ambiguous 189 | _String("Failed to resize memory to '") & new_size & "' bytes'", true); | ^~~~~~~~ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include/hy_strings.h:127:3: note: candidate constructor 127 | _String(long const number); | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include/hy_strings.h:140:3: note: candidate constructor 140 | _String(const unsigned long sL, char *buffer = nil); | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include/hy_strings.h:151:3: note: candidate constructor 151 | _String(const hyFloat number, const char *format = nil); | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/include/hy_strings.h:245:3: note: candidate constructor 245 | _String(const char c); | ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/global_things.cpp:512:25: warning: format string is not a string literal [-Wformat-nonliteral] 512 | fprintf(stderr, messages[file_index], prefix[file_index]->get_str()); | ^~~~~~~~~~~~~~~~~~~~ 1 warning and 2 errors generated. ninja: build stopped: subcommand failed. *** Error code 1 Stop. make: stopped in /usr/ports/biology/hyphy
