=>> Building biology/iqtree build started at Sun Apr 7 08:28:41 BST 2024 port directory: /usr/ports/biology/iqtree package name: iqtree-2.2.2.7 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: jrm@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1183 Sep 5 2023 /usr/ports/biology/iqtree/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: 8a1ec0de6b Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 02 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 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=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-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/13-amd64-default-dan/02/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 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 iqtree-2.2.2.7: EXAMPLES=on: Build and/or install examples ===> 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/iqtree/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/iqtree/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/iqtree/work/.cache HOME=/wrkdirs/usr/ports/biology/iqtree/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/iqtree/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/iqtree/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCACHE_DIR="/root/.ccache" --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/iqtree/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/iqtree/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/iqtree/work/.cache HOME=/wrkdirs/usr/ports/biology/iqtree/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/iqtree/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/iqtree/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/iqtree/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CCACHE_DIR="/root/.ccache" 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-- PORTEXAMPLES="" CMAKE_BUILD_TYPE="release" OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/iqtree" EXAMPLESDIR="share/examples/iqtree" DATADIR="share/iqtree" WWWDIR="www/iqtree" ETCDIR="etc/iqtree" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/iqtree DOCSDIR=/usr/local/share/doc/iqtree EXAMPLESDIR=/usr/local/share/examples/iqtree WWWDIR=/usr/local/www/iqtree ETCDIR=/usr/local/etc/iqtree --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 mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/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 --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 ===> iqtree-2.2.2.7 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> iqtree-2.2.2.7 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of iqtree-2.2.2.7 =========================================================================== =================================================== ===== 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 iqtree-2.2.2.7 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by iqtree-2.2.2.7 for building => SHA256 Checksum OK for iqtree-iqtree2-v2.2.2.7_GH0.tar.gz. => SHA256 Checksum OK for tothuhien-lsd2-26ba127_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 iqtree-2.2.2.7 for building ===> Extracting for iqtree-2.2.2.7 => SHA256 Checksum OK for iqtree-iqtree2-v2.2.2.7_GH0.tar.gz. => SHA256 Checksum OK for tothuhien-lsd2-26ba127_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 iqtree-2.2.2.7 ===> Applying FreeBSD patches for iqtree-2.2.2.7 from /usr/ports/biology/iqtree/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> iqtree-2.2.2.7 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.28.3.pkg [pkg-builder.dan.net.uk] Installing cmake-core-3.28.3... [pkg-builder.dan.net.uk] `-- Installing expat-2.6.1... [pkg-builder.dan.net.uk] `-- Extracting expat-2.6.1: .......... done [pkg-builder.dan.net.uk] `-- Installing jsoncpp-1.9.5... [pkg-builder.dan.net.uk] `-- Extracting jsoncpp-1.9.5: .......... done [pkg-builder.dan.net.uk] `-- Installing libuv-1.48.0... [pkg-builder.dan.net.uk] `-- Extracting libuv-1.48.0: .......... done [pkg-builder.dan.net.uk] `-- Installing openssl-3.0.13_1,1... [pkg-builder.dan.net.uk] `-- Extracting openssl-3.0.13_1,1: .......... done [pkg-builder.dan.net.uk] `-- Installing rhash-1.4.4_1... [pkg-builder.dan.net.uk] | `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] | `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] `-- Extracting rhash-1.4.4_1: .......... done [pkg-builder.dan.net.uk] Extracting cmake-core-3.28.3: .......... done ===> iqtree-2.2.2.7 depends on file: /usr/local/bin/cmake - found ===> Returning to build of iqtree-2.2.2.7 ===> iqtree-2.2.2.7 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.11.1,2.pkg [pkg-builder.dan.net.uk] Installing ninja-1.11.1,2... [pkg-builder.dan.net.uk] `-- Installing python39-3.9.18_1... [pkg-builder.dan.net.uk] | `-- Installing libffi-3.4.4_1... [pkg-builder.dan.net.uk] | `-- Extracting libffi-3.4.4_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing mpdecimal-2.5.1... [pkg-builder.dan.net.uk] | `-- Extracting mpdecimal-2.5.1: .......... done [pkg-builder.dan.net.uk] | `-- Installing readline-8.2.10... [pkg-builder.dan.net.uk] | `-- Extracting readline-8.2.10: .......... done [pkg-builder.dan.net.uk] `-- Extracting python39-3.9.18_1: .......... done [pkg-builder.dan.net.uk] Extracting ninja-1.11.1,2: ..... done ===== Message from python39-3.9.18_1: -- 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 ===> iqtree-2.2.2.7 depends on executable: ninja - found ===> Returning to build of iqtree-2.2.2.7 ===> iqtree-2.2.2.7 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - not found ===> Installing existing package /packages/All/eigen-3.4.0_3.pkg [pkg-builder.dan.net.uk] Installing eigen-3.4.0_3... [pkg-builder.dan.net.uk] `-- Installing blas-3.12.0_1... [pkg-builder.dan.net.uk] | `-- Installing gcc13-13.2.0_4... [pkg-builder.dan.net.uk] | | `-- Installing binutils-2.40_5,1... [pkg-builder.dan.net.uk] | | `-- Installing zstd-1.5.5_1... [pkg-builder.dan.net.uk] | | | `-- Installing liblz4-1.9.4_1,1... [pkg-builder.dan.net.uk] | | | `-- Extracting liblz4-1.9.4_1,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting zstd-1.5.5_1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting binutils-2.40_5,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing gmp-6.3.0... [pkg-builder.dan.net.uk] | | `-- Extracting gmp-6.3.0: .......... done [pkg-builder.dan.net.uk] | | `-- Installing mpc-1.3.1_1... [pkg-builder.dan.net.uk] | | `-- Installing mpfr-4.2.1,1... [pkg-builder.dan.net.uk] | | `-- Extracting mpfr-4.2.1,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting mpc-1.3.1_1: ...... done [pkg-builder.dan.net.uk] | `-- Extracting gcc13-13.2.0_4: .......... done create symlink for gcc13 create symlink for gcc13 (world) create symlink for g++13 create symlink for g++13 (world) create symlink for cpp13 create symlink for cpp13 (world) [pkg-builder.dan.net.uk] `-- Extracting blas-3.12.0_1: ..... done [pkg-builder.dan.net.uk] `-- Installing lapack-3.12.0_2... [pkg-builder.dan.net.uk] `-- Extracting lapack-3.12.0_2: .......... done [pkg-builder.dan.net.uk] Extracting eigen-3.4.0_3: .......... done ===== Message from gcc13-13.2.0_4: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc13 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> iqtree-2.2.2.7 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found ===> Returning to build of iqtree-2.2.2.7 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> iqtree-2.2.2.7 depends on shared library: libboost_filesystem.so - not found ===> Installing existing package /packages/All/boost-libs-1.84.0.pkg [pkg-builder.dan.net.uk] Installing boost-libs-1.84.0... [pkg-builder.dan.net.uk] `-- Installing icu-74.2,1... [pkg-builder.dan.net.uk] `-- Extracting icu-74.2,1: .......... done [pkg-builder.dan.net.uk] Extracting boost-libs-1.84.0: .......... done ===== Message from boost-libs-1.84.0: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> iqtree-2.2.2.7 depends on shared library: libboost_filesystem.so - found (/usr/local/lib/libboost_filesystem.so) ===> Returning to build of iqtree-2.2.2.7 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for iqtree-2.2.2.7 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/iqtree/work/.build CMake Deprecation Warning at CMakeLists.txt:58 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is Clang 14.0.5 -- The CXX compiler identification is Clang 14.0.5 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /ccache/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: /ccache/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Boost: /usr/local/include (found version "1.84.0") IQ-TREE flags : Build mode : Release Target OS : Unix Compiler : Clang Compiler version: 14.0.5 Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 C flags : -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -O3 -ffunction-sections -fdata-sections CXX flags : -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -ffunction-sections -fdata-sections LINKER flags : -fstack-protector-strong -rdynamic -Wl,--gc-sections -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for backtrace -- Looking for backtrace - not found -- Found Backtrace: /usr/lib/libexecinfo.so -- Found ZLIB: /usr/lib/libz.so (found version "1.2.13") Using system zlib CMake Deprecation Warning at yaml-cpp/CMakeLists.txt:5 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Performing Test FLAG_WEXTRA -- Performing Test FLAG_WEXTRA - Success CMake Deprecation Warning at terraphast/CMakeLists.txt:3 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- clang-tidy not found. -- Configuring done (4.7s) -- 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/iqtree/work/.build =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for iqtree-2.2.2.7 [ 0% 1/286] /ccache/libexec/ccache/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_LSD2 -D_USE_PTHREADS -I/wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7 -I/wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/yaml-cpp/include 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-I/wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7 -I/wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/yaml-cpp/include -I/wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/after -I/wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/system -I/usr/local/include -I/wrkdirs/usr/ports/biology/iqtree/work/.build -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -D__AVX -mavx -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/tree/phylotreeavx.cpp [ 1% 4/286] : && /usr/local/bin/cmake -E rm -f libkernelavx.a && /usr/bin/llvm-ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o && /usr/bin/llvm-ranlib libkernelavx.a && : [ 1% 5/286] /ccache/libexec/ccache/c++ 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/usr/local/include/boost/math/distributions/binomial.hpp:83: In file included from /usr/local/include/boost/math/special_functions/beta.hpp:13: In file included from /usr/local/include/boost/math/special_functions/math_fwd.hpp:29: In file included from /usr/local/include/boost/math/special_functions/detail/round_fwd.hpp:11: /usr/local/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings] # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" ^ 1 warning generated. 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-I/wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/yaml-cpp/include -I/wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/after -I/wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/system -I/usr/local/include -I/wrkdirs/usr/ports/biology/iqtree/work/.build -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o -MF lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o.d -o lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o -c /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lsd2/src/readData.cpp [ 98% 283/286] /ccache/libexec/ccache/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_LSD2 -D_USE_PTHREADS -I/wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7 -I/wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/yaml-cpp/include 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lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o lsd2/CMakeFiles/lsd2.dir/src/utils.cpp.o && /usr/bin/llvm-ranlib lsd2/liblsd2.a && : [ 99% 285/286] : && /usr/local/bin/cmake -E rm -f main/libmain.a && /usr/bin/llvm-ar qc main/libmain.a main/CMakeFiles/main.dir/main.cpp.o main/CMakeFiles/main.dir/phyloanalysis.cpp.o main/CMakeFiles/main.dir/phylotesting.cpp.o main/CMakeFiles/main.dir/treetesting.cpp.o main/CMakeFiles/main.dir/timetree.cpp.o main/CMakeFiles/main.dir/alisim.cpp.o main/CMakeFiles/main.dir/terraceanalysis.cpp.o && /usr/bin/llvm-ranlib main/libmain.a && : [100% 286/286] : && /ccache/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -ffunction-sections -fdata-sections -fstack-protector-strong -rdynamic -Wl,--gc-sections CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2 -lexecinfo booster/libbooster.a pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a simulator/libsimulator.a terrace/libterrace.a yaml-cpp/libyaml-cpp.a phylo-yaml/libphyloYAML.a main/libmain.a -lm terracetphast/libterracetphast.a lsd2/liblsd2.a libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a yaml-cpp/libyaml-cpp.a booster/libbooster.a pda/libpda.a nclextra/libnclextra.a whtest/libwhtest.a vectorclass/libvectorclass.a terrace/libterrace.a tree/libtree.a pll/libpll.a alignment/libalignment.a simulator/libsimulator.a alignment/libalignment.a simulator/libsimulator.a ncl/libncl.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a sprng/libsprng.a -lz gsl/libgsl.a terraphast/libterraphast.a && cd /wrkdirs/usr/ports/biology/iqtree/work/.build && strip /wrkdirs/usr/ports/biology/iqtree/work/.build/iqtree2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for iqtree-2.2.2.7 ===> Generating temporary packing list install -s -m 555 /wrkdirs/usr/ports/biology/iqtree/work/.build/iqtree2 /wrkdirs/usr/ports/biology/iqtree/work/stage/usr/local/bin/iqtree install -m 0644 /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/example/* /wrkdirs/usr/ports/biology/iqtree/work/stage/usr/local/share/examples/iqtree ====> 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=2024-04-07T07:28:41+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=8a1ec0de6b' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for iqtree-2.2.2.7 ===> Building iqtree-2.2.2.7 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for iqtree-2.2.2.7 build of biology/iqtree | iqtree-2.2.2.7 ended at Sun Apr 7 12:03:18 BST 2024 build time: 03:34:38