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Maintainer: j...@freebsd.org Log URL: https://pkg-status.freebsd.org/ampere3/data/131releng-armv7-default/0363347cf562/logs/hyphy-2.5.51.h.log Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=131releng-armv7-default&build=0363347cf562 Log: =>> Building biology/hyphy build started at Wed Jun 7 08:26:21 UTC 2023 port directory: /usr/ports/biology/hyphy package name: hyphy-2.5.51.h building for: FreeBSD 131releng-armv7-default-job-06 13.1-RELEASE-p7 FreeBSD 13.1-RELEASE-p7 1301000 arm maintained by: j...@freebsd.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400073 Jail OSVERSION: 1301000 Job Id: 06 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1301000 UNAME_v=FreeBSD 13.1-RELEASE-p7 1301000 UNAME_r=13.1-RELEASE-p7 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 LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-23-ga7f8d188 MASTERMNT=/usr/local/poudriere/data/.m/131releng-armv7-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/131releng-armv7-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=131releng-armv7-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/131releng-armv7-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for hyphy-2.5.51.h: AVX=off: Advanced vector extensions support ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- j...@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=" -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -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" --End MAKE_ENV-- --PLIST_SUB-- CMAKE_BUILD_TYPE="release" OSREL=13.1 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 #### /usr/local/etc/poudriere.d/make.conf #### # 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 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 13.0.0 (g...@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: armv7-unknown-freebsd13.1-gnueabihf Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 13.0.0 (g...@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: armv7-unknown-freebsd13.1-gnueabihf Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_53255a77=yes CC_OUTPUT_921dbbb2_911cfe02=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes CC_OUTPUT_921dbbb2_af59ad06=yes CC_OUTPUT_921dbbb2_a15f3fcf=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 13.0.0 (g...@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: armv7-unknown-freebsd13.1-gnueabihf Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=armv7 OPSYS=FreeBSD _OSRELEASE=13.1-RELEASE-p7 OSREL=13.1 OSVERSION=1301000 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### 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) 1048576 stack size (kbytes, -s) 1048576 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) 1024 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 --End resource limits-- =======================<phase: check-sanity >============================ ===> License MIT accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> hyphy-2.5.51.h depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.19.1_1.pkg [131releng-armv7-default-job-06] Installing pkg-1.19.1_1... [131releng-armv7-default-job-06] Extracting pkg-1.19.1_1: .......... done ===> hyphy-2.5.51.h depends on file: /usr/local/sbin/pkg - found ===> Returning to build of hyphy-2.5.51.h =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by hyphy-2.5.51.h for building =========================================================================== =======================<phase: checksum >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by hyphy-2.5.51.h for building => SHA256 Checksum OK for veg-hyphy-2.5.51hf_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by hyphy-2.5.51.h for building ===> Extracting for hyphy-2.5.51.h => SHA256 Checksum OK for veg-hyphy-2.5.51hf_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for hyphy-2.5.51.h =========================================================================== =======================<phase: build-depends >============================ ===> hyphy-2.5.51.h depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.26.1_1.pkg [131releng-armv7-default-job-06] Installing cmake-core-3.26.1_1... [131releng-armv7-default-job-06] `-- Installing expat-2.5.0... [131releng-armv7-default-job-06] `-- Extracting expat-2.5.0: .......... done [131releng-armv7-default-job-06] `-- Installing jsoncpp-1.9.5... [131releng-armv7-default-job-06] `-- Extracting jsoncpp-1.9.5: .......... done [131releng-armv7-default-job-06] `-- Installing libuv-1.45.0... [131releng-armv7-default-job-06] `-- Extracting libuv-1.45.0: .......... done [131releng-armv7-default-job-06] `-- Installing rhash-1.4.3... [131releng-armv7-default-job-06] | `-- Installing gettext-runtime-0.21.1... [131releng-armv7-default-job-06] | | `-- Installing indexinfo-0.3.1... [131releng-armv7-default-job-06] | | `-- Extracting indexinfo-0.3.1: .... done [131releng-armv7-default-job-06] | `-- Extracting gettext-runtime-0.21.1: .......... done [131releng-armv7-default-job-06] `-- Extracting rhash-1.4.3: .......... done [131releng-armv7-default-job-06] Extracting cmake-core-3.26.1_1: .......... done ===> hyphy-2.5.51.h depends on file: /usr/local/bin/cmake - found ===> Returning to build of hyphy-2.5.51.h ===> hyphy-2.5.51.h depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.11.1,2.pkg [131releng-armv7-default-job-06] Installing ninja-1.11.1,2... [131releng-armv7-default-job-06] `-- Installing python39-3.9.16_2... [131releng-armv7-default-job-06] | `-- Installing libffi-3.4.4... [131releng-armv7-default-job-06] | `-- Extracting libffi-3.4.4: .......... done [131releng-armv7-default-job-06] | `-- Installing mpdecimal-2.5.1... [131releng-armv7-default-job-06] | `-- Extracting mpdecimal-2.5.1: .......... done [131releng-armv7-default-job-06] | `-- Installing readline-8.2.1... [131releng-armv7-default-job-06] | `-- Extracting readline-8.2.1: .......... done [131releng-armv7-default-job-06] `-- Extracting python39-3.9.16_2: .......... done [131releng-armv7-default-job-06] Extracting ninja-1.11.1,2: ........ done ===== Message from python39-3.9.16_2: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===> hyphy-2.5.51.h depends on executable: ninja - found ===> Returning to build of hyphy-2.5.51.h =========================================================================== =======================<phase: lib-depends >============================ ===> hyphy-2.5.51.h depends on shared library: libcurl.so - not found ===> Installing existing package /packages/All/curl-8.1.1.pkg [131releng-armv7-default-job-06] Installing curl-8.1.1... [131releng-armv7-default-job-06] `-- Installing ca_root_nss-3.89.1... [131releng-armv7-default-job-06] `-- Extracting ca_root_nss-3.89.1: .......... done [131releng-armv7-default-job-06] `-- Installing libnghttp2-1.53.0... [131releng-armv7-default-job-06] `-- Extracting libnghttp2-1.53.0: .......... done [131releng-armv7-default-job-06] `-- Installing libpsl-0.21.2_3... [131releng-armv7-default-job-06] | `-- Installing libidn2-2.3.4... [131releng-armv7-default-job-06] | | `-- Installing libunistring-1.1... [131releng-armv7-default-job-06] | | `-- Extracting libunistring-1.1: .......... done [131releng-armv7-default-job-06] | `-- Extracting libidn2-2.3.4: .......... done [131releng-armv7-default-job-06] `-- Extracting libpsl-0.21.2_3: .......... done [131releng-armv7-default-job-06] `-- Installing libssh2-1.11.0,3... [131releng-armv7-default-job-06] `-- Extracting libssh2-1.11.0,3: .......... done [131releng-armv7-default-job-06] Extracting curl-8.1.1: .......... done ===== Message from ca_root_nss-3.89.1: -- 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 ===> hyphy-2.5.51.h depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> Returning to build of hyphy-2.5.51.h =========================================================================== =======================<phase: configure >============================ ===> Configuring for hyphy-2.5.51.h ===> Performing in-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf -- The C compiler identification is Clang 13.0.0 -- The CXX compiler identification is Clang 13.0.0 -- 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_SSE4_EXTENSIONS -- Performing Test HAVE_SSE4_EXTENSIONS - Failed -- Performing Test HAVE_NEON_EXTENSIONS -- Performing Test HAVE_NEON_EXTENSIONS - Failed Set default compiler flags to -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -std=c++14 -Wall -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) -- Found CURL: /usr/local/lib/libcurl.so (found version "8.1.1") /usr/local/lib/libcurl.so -- Found ZLIB: /usr/lib/libz.so (found suitable version "1.2.12", minimum required is "1.2.9") Node not installed; API documentation will not be generated -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- Configuring done (2.9s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_COLOR_MAKEFILE CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE FETCHCONTENT_FULLY_DISCONNECTED THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf =========================================================================== =======================<phase: build >============================ ===> Building for hyphy-2.5.51.h [ 1% 2/67] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/contrib/SQLite-3.8.2 -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 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -std=c++14 -Wall -w -Weffc++ -Wextra -Wall -g -Weffc++ -Wextra -Wall -std=c++14 -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/_hyExecutionCo ntext.cpp.o -MF CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/src/core/_hyExecutionContext.cpp [ 2% 3/67] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/contrib/SQLite-3.8.2 -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 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -std=c++14 -Wall -w -Weffc++ -Wextra -Wall -g -Weffc++ -Wextra -Wall -std=c++14 -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -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-2.5.51hf/src/core/alignment.cpp FAILED: CMakeFiles/hyphy.dir/src/core/alignment.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/contrib/SQLite-3.8.2 -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 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -std=c++14 -Wall -w -Weffc++ -Wextra -Wall -g -Weffc++ -Wextra -Wall -std=c++14 -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -MF CMakeF iles/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-2.5.51hf/src/core/alignment.cpp In file included from /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/src/core/alignment.cpp:44: In file included from /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/src/core/include/alignment.h:44: /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/src/core/include/likefunc.h:285:17: error: class member cannot be redeclared void SetThreadCount (long) { ^ /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/src/core/include/likefunc.h:278:17: note: previous definition is here void SetThreadCount (long tc) { ^ 1 error generated. [ 4% 3/67] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/contrib/SQLite-3.8.2 -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 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -std=c++14 -Wall -w -Weffc++ -Wextra -Wall -g -Weffc++ -Wextra -Wall -std=c++14 -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/associative_li st.cpp.o -MF CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.51hf/src/core/associative_list.cpp ninja: build stopped: subcommand failed. ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /usr/ports/biology/hyphy
