Date: Tue, 23 Nov 2021 04:04:04 GMT From: pkg-fallout@FreeBSD.org To: jrm@FreeBSD.org Cc: pkg-fallout@FreeBSD.org Subject: [package - main-i386-default][biology/hyphy] Failed for hyphy-2.5.33 in build Message-ID: <202111230404.1AN444rU015732@beefy17.nyi.freebsd.org>
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You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: jrm@FreeBSD.org Log URL: http://beefy17.nyi.freebsd.org/data/main-i386-default/p23db194e7338_sb92f4ae58a/logs/hyphy-2.5.33.log Build URL: http://beefy17.nyi.freebsd.org/build.html?mastername=main-i386-default&build=p23db194e7338_sb92f4ae58a Log: =>> Building biology/hyphy build started at Tue Nov 23 04:03:54 UTC 2021 port directory: /usr/ports/biology/hyphy package name: hyphy-2.5.33 building for: FreeBSD main-i386-default-job-05 14.0-CURRENT FreeBSD 14.0-CURRENT 1400042 i386 maintained by: jrm@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-21-g883afb07 Host OSVERSION: 1400008 Jail OSVERSION: 1400042 Job Id: 05 !!! Jail is newer than host. (Jail: 1400042, Host: 1400008) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh UNAME_p=i386 UNAME_m=i386 OSVERSION=1400042 UNAME_v=FreeBSD 14.0-CURRENT 1400042 UNAME_r=14.0-CURRENT 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=3.2.8-21-g883afb07 MASTERMNT=/usr/local/poudriere/data/.m/main-i386-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-i386-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-i386-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-i386-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-2.5.33: AVX=off: Advanced vector extensions support ===> 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 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 NO_PIE=yes 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=14.0 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} #### /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 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: i386-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: i386-unknown-freebsd14.0 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" "-m" "elf_i386_fbsd" "-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_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: i386-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=i386 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400042 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) 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) 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-2.5.33 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.17.5.pkg [main-i386-default-job-05] Installing pkg-1.17.5... [main-i386-default-job-05] Extracting pkg-1.17.5: .......... done ===> hyphy-2.5.33 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of hyphy-2.5.33 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by hyphy-2.5.33 for building =========================================================================== =======================<phase: checksum >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by hyphy-2.5.33 for building => SHA256 Checksum OK for veg-hyphy-2.5.33_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by hyphy-2.5.33 for building ===> Extracting for hyphy-2.5.33 => SHA256 Checksum OK for veg-hyphy-2.5.33_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for hyphy-2.5.33 =========================================================================== =======================<phase: build-depends >============================ ===> hyphy-2.5.33 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.21.4_1.pkg [main-i386-default-job-05] Installing cmake-3.21.4_1... [main-i386-default-job-05] `-- Installing curl-7.80.0... [main-i386-default-job-05] | `-- Installing ca_root_nss-3.71... [main-i386-default-job-05] | `-- Extracting ca_root_nss-3.71: ........ done [main-i386-default-job-05] | `-- Installing libnghttp2-1.46.0... [main-i386-default-job-05] | `-- Extracting libnghttp2-1.46.0: .......... done [main-i386-default-job-05] | `-- Installing libssh2-1.9.0_3,3... [main-i386-default-job-05] | `-- Extracting libssh2-1.9.0_3,3: .......... done [main-i386-default-job-05] `-- Extracting curl-7.80.0: .......... done [main-i386-default-job-05] `-- Installing expat-2.4.1... [main-i386-default-job-05] `-- Extracting expat-2.4.1: .......... done [main-i386-default-job-05] `-- Installing jsoncpp-1.9.5... [main-i386-default-job-05] `-- Extracting jsoncpp-1.9.5: .......... done [main-i386-default-job-05] `-- Installing libarchive-3.5.1,1... [main-i386-default-job-05] | `-- Installing liblz4-1.9.3,1... [main-i386-default-job-05] | `-- Extracting liblz4-1.9.3,1: .......... done [main-i386-default-job-05] `-- Extracting libarchive-3.5.1,1: .......... done [main-i386-default-job-05] `-- Installing libuv-1.42.0... [main-i386-default-job-05] `-- Extracting libuv-1.42.0: .......... done [main-i386-default-job-05] `-- Installing rhash-1.4.2... [main-i386-default-job-05] | `-- Installing gettext-runtime-0.21... [main-i386-default-job-05] | | `-- Installing indexinfo-0.3.1... [main-i386-default-job-05] | | `-- Extracting indexinfo-0.3.1: .... done [main-i386-default-job-05] | `-- Extracting gettext-runtime-0.21: .......... done [main-i386-default-job-05] `-- Extracting rhash-1.4.2: .......... done [main-i386-default-job-05] Extracting cmake-3.21.4_1: .......... done ===== Message from ca_root_nss-3.71: -- 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-2.5.33 depends on file: /usr/local/bin/cmake - found ===> Returning to build of hyphy-2.5.33 ===> hyphy-2.5.33 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.10.2,2.pkg [main-i386-default-job-05] Installing ninja-1.10.2,2... [main-i386-default-job-05] `-- Installing python38-3.8.12_1... [main-i386-default-job-05] | `-- Installing libffi-3.3_1... [main-i386-default-job-05] | `-- Extracting libffi-3.3_1: .......... done [main-i386-default-job-05] | `-- Installing mpdecimal-2.5.1... [main-i386-default-job-05] | `-- Extracting mpdecimal-2.5.1: .......... done [main-i386-default-job-05] | `-- Installing readline-8.1.1... [main-i386-default-job-05] | `-- Extracting readline-8.1.1: .......... done [main-i386-default-job-05] `-- Extracting python38-3.8.12_1: .......... done [main-i386-default-job-05] Extracting ninja-1.10.2,2: ........ done ===== Message from python38-3.8.12_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py38-gdbm databases/py-gdbm@py38 py38-sqlite3 databases/py-sqlite3@py38 py38-tkinter x11-toolkits/py-tkinter@py38 ===> hyphy-2.5.33 depends on executable: ninja - found ===> Returning to build of hyphy-2.5.33 =========================================================================== =======================<phase: lib-depends >============================ ===> hyphy-2.5.33 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) =========================================================================== =======================<phase: configure >============================ ===> Configuring for hyphy-2.5.33 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/hyphy/work/.build -- 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_SSE3_EXTENSIONS -- Performing Test HAVE_SSE3_EXTENSIONS - Success -- Performing Test HAVE_NEON_EXTENSIONS -- Performing Test HAVE_NEON_EXTENSIONS - Failed Set compiler flags to -fsigned-char -O3 -msse3 -- Found OpenMP_C: -fopenmp=libomp (found version "5.0") -- Found OpenMP_CXX: -fopenmp=libomp (found version "5.0") -- Found OpenMP: TRUE (found version "5.0") -- Found CURL: /usr/local/lib/libcurl.so (found version "7.80.0") /usr/local/lib/libcurl.so -- Found ZLIB: /usr/lib/libz.so (found suitable version "1.2.11", 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 -- Generating done 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 THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/biology/hyphy/work/.build =========================================================================== =======================<phase: build >============================ ===> Building for hyphy-2.5.33 [ 1% 2/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/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 -fsigned-char -O3 -msse3 -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -MF CMakeFiles/hyphy.dir/src/core/_hyE xecutionContext.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/core/_hyExecutionContext.cpp [ 3% 3/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/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 -fsigned-char -O3 -msse3 -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -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-2.5.33/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_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-2.5.33/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/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 -fsigned-char -O3 -msse3 -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -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 CMake Files/hyphy.dir/src/core/alignment.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/core/alignment.cpp In file included from /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/core/alignment.cpp:44: In file included from /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/core/include/alignment.h:44: In file included from /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/core/include/likefunc.h:44: In file included from /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/core/include/category.h:44: In file included from /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/core/include/batchlan.h:47: In file included from /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/core/include/dataset.h:47: /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/core/include/function_templates.h:160:15: error: duplicate directives 'unroll_count(8)' and '#pragma unroll(4)' #pragma GCC unroll 4 ^ 1 error generated. [ 4% 3/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/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 -fsigned-char -O3 -msse3 -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -MF CMakeFiles/hyphy.dir/src/core/associa tive_list.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/core/associative_list.cpp FAILED: CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/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 -fsigned-char -O3 -msse3 -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -MF CMakeFiles/hyphy.dir/src/core/associative_list.cp p.o.d -o CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/core/associative_list.cpp In file included from /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/core/associative_list.cpp:62: In file included from /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/core/include/global_object_lists.h:42: In file included from /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/core/include/dataset_filter.h:44: In file included from /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/core/include/dataset.h:47: /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.33/src/core/include/function_templates.h:160:15: error: duplicate directives 'unroll_count(8)' and '#pragma unroll(4)' #pragma GCC unroll 4 ^ 1 error generated. 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
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