=>> Building biology/hyphy build started at Wed May 7 14:23:00 BST 2025 port directory: /usr/ports/biology/hyphy package name: hyphy-2.5.70 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: jrm@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 648 Mar 28 09:38 /usr/ports/biology/hyphy/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: 1367bc51cd Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 08 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE UNAME_r=14.2-RELEASE 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/14-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/08/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=14-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/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-2.5.70: 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 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 " 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 FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl apache=2.4 imagemagick=7 java=21 linux=c7 mysql=8.0 php=8.3 samba=4.19 varnish=7 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE ALLOW_UNSUPPORTED_SYSTEM=yes WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### 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) 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-2.5.70 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.1.2.pkg [pkg-builder.dan.net.uk] Installing pkg-2.1.2... [pkg-builder.dan.net.uk] Extracting pkg-2.1.2: .......... done ===> hyphy-2.5.70 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of hyphy-2.5.70 =========================================================================== =================================================== ===== 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-2.5.70 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by hyphy-2.5.70 for building => SHA256 Checksum OK for veg-hyphy-2.5.70_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-2.5.70 for building ===> Extracting for hyphy-2.5.70 => SHA256 Checksum OK for veg-hyphy-2.5.70_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-2.5.70 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> hyphy-2.5.70 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.6.pkg [pkg-builder.dan.net.uk] Installing cmake-core-3.31.6... [pkg-builder.dan.net.uk] `-- Installing expat-2.7.1... [pkg-builder.dan.net.uk] `-- Extracting expat-2.7.1: .......... done [pkg-builder.dan.net.uk] `-- Installing jsoncpp-1.9.6_1... [pkg-builder.dan.net.uk] `-- Extracting jsoncpp-1.9.6_1: .......... done [pkg-builder.dan.net.uk] `-- Installing libidn2-2.3.8... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1_1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1_1: . done [pkg-builder.dan.net.uk] | `-- Installing libunistring-1.3... [pkg-builder.dan.net.uk] | `-- Extracting libunistring-1.3: .......... done [pkg-builder.dan.net.uk] `-- Extracting libidn2-2.3.8: .......... done [pkg-builder.dan.net.uk] `-- Installing libuv-1.51.0... [pkg-builder.dan.net.uk] `-- Extracting libuv-1.51.0: .......... done [pkg-builder.dan.net.uk] `-- Installing openssl-3.0.16,1... [pkg-builder.dan.net.uk] `-- Extracting openssl-3.0.16,1: .......... done [pkg-builder.dan.net.uk] `-- Installing rhash-1.4.4_1... [pkg-builder.dan.net.uk] | `-- Installing gettext-runtime-0.23.1... [pkg-builder.dan.net.uk] | `-- Extracting gettext-runtime-0.23.1: .......... done [pkg-builder.dan.net.uk] `-- Extracting rhash-1.4.4_1: .......... done [pkg-builder.dan.net.uk] Extracting cmake-core-3.31.6: .......... done ===> hyphy-2.5.70 depends on file: /usr/local/bin/cmake - found ===> Returning to build of hyphy-2.5.70 ===> hyphy-2.5.70 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.11.1,4.pkg [pkg-builder.dan.net.uk] Installing ninja-1.11.1,4... [pkg-builder.dan.net.uk] `-- Installing python311-3.11.12... [pkg-builder.dan.net.uk] | `-- Installing libffi-3.4.8... [pkg-builder.dan.net.uk] | `-- Extracting libffi-3.4.8: .......... done [pkg-builder.dan.net.uk] | `-- Installing mpdecimal-4.0.0... [pkg-builder.dan.net.uk] | `-- Extracting mpdecimal-4.0.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing readline-8.2.13_2... [pkg-builder.dan.net.uk] | `-- Extracting readline-8.2.13_2: .......... done [pkg-builder.dan.net.uk] `-- Extracting python311-3.11.12: .......... done [pkg-builder.dan.net.uk] Extracting ninja-1.11.1,4: ..... done ===== Message from python311-3.11.12: -- 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-2.5.70 depends on executable: ninja - found ===> Returning to build of hyphy-2.5.70 ===> hyphy-2.5.70 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg-builder.dan.net.uk] Installing ccache-3.7.12_8... [pkg-builder.dan.net.uk] 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-2.5.70 depends on file: /usr/local/bin/ccache - found ===> Returning to build of hyphy-2.5.70 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> hyphy-2.5.70 depends on shared library: libcurl.so - not found ===> Installing existing package /packages/All/curl-8.13.0_1.pkg [pkg-builder.dan.net.uk] Installing curl-8.13.0_1... [pkg-builder.dan.net.uk] `-- Installing brotli-1.1.0,1... [pkg-builder.dan.net.uk] `-- Extracting brotli-1.1.0,1: .......... done [pkg-builder.dan.net.uk] `-- Installing libnghttp2-1.65.0... [pkg-builder.dan.net.uk] `-- Extracting libnghttp2-1.65.0: ....... done [pkg-builder.dan.net.uk] `-- Installing libssh2-1.11.1,3... [pkg-builder.dan.net.uk] `-- Extracting libssh2-1.11.1,3: .......... done [pkg-builder.dan.net.uk] `-- Installing zstd-1.5.7... [pkg-builder.dan.net.uk] | `-- Installing liblz4-1.10.0,1... [pkg-builder.dan.net.uk] | `-- Extracting liblz4-1.10.0,1: .......... done [pkg-builder.dan.net.uk] `-- Extracting zstd-1.5.7: .......... done [pkg-builder.dan.net.uk] Extracting curl-8.13.0_1: .......... done ===> hyphy-2.5.70 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> Returning to build of hyphy-2.5.70 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for hyphy-2.5.70 ===> Performing in-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.70 -- The C compiler identification is Clang 18.1.6 -- The CXX compiler identification is Clang 18.1.6 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/local/libexec/ccache/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/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAVE_SSE4_EXTENSIONS -- Performing Test HAVE_SSE4_EXTENSIONS - Success -- Performing Test HAVE_NEON_EXTENSIONS -- Performing Test HAVE_NEON_EXTENSIONS - Failed Set compiler flags to -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -std=c++14 -Wall -msse4.1 -g Set linker flags to -g -- Could NOT find BLAS (missing: BLAS_LIBRARIES) -- Found OpenMP_C: -fopenmp=libomp (found version "5.1") -- Found OpenMP_CXX: -fopenmp=libomp (found version "5.1") -- Found OpenMP: TRUE (found version "5.1") -- Found CURL: /usr/local/lib/libcurl.so (found version "8.13.0") /usr/local/lib/libcurl.so -- Found ZLIB: /usr/lib/libz.so (found suitable version "1.3.1", minimum required is "1.2.9") Node not installed; API documentation will not be generated /usr/local/share/hyphy -- 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) CMake Warning (dev) at CMakeLists.txt:675 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:678 (makeLink) This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring done (1.9s) -- 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-2.5.70 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for hyphy-2.5.70 [ 1% 1/68] /usr/local/libexec/ccache/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-2.5.70/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.70/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.70/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.70/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.70/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 -msse4.1 -g -w -Weffc++ -Wextra -Wall -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.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-2.5.70/src/core/_hyExecutionContext.cpp [ 2% 2/68] /usr/local/libexec/ccache/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-2.5.70/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.70/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.70/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.70/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.70/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 -msse4.1 -g -w -Weffc++ -Wextra -Wall -fopenmp=libomp -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-2.5.70/src/core/alignment.cpp [ 4% 3/68] /usr/local/libexec/ccache/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-2.5.70/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.70/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.70/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.70/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.70/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 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/usr/local/lib/libcurl.so /usr/lib/libz.so /usr/lib/libomp.so && cd /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.70 && ln -sf hyphy HYPHYMP =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for hyphy-2.5.70 ===> Generating temporary packing list [ 0% 1/1] cd /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.70 && /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/SubstitutionClasses -- Installing: 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/wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECM -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECMu -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/reducedREV.mdl -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/ECM+MLFREQS.mdl -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/RNAEqualInput -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/MG94customCF3x4.mdl -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/fitness.mdl -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/MG94x2.mdl -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAA.mdl -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/GY94.ibf -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin+F.mdl -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/MG94with9freqs.mdl -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.mdl -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/MG94.mdl -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAUserFreqs.mdl -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters2.mdl -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/ECM+F.mdl -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/190 -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/F81.mdl -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/RNAREV_1 -- Installing: /wrkdirs/usr/ports/biology/hyphy/work/stage/usr/local/share/hyphy/TemplateBatchFiles/TemplateModels/RNA16SvH.mdl -- Installing: /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/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=2025-05-07T13:23:00+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=1367bc51cd' '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-2.5.70 ===> Building hyphy-2.5.70 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for hyphy-2.5.70 build of biology/hyphy | hyphy-2.5.70 ended at Wed May 7 14:26:31 BST 2025 build time: 00:03:31