=>> Building biology/hhsuite build started at Tue May 6 19:14:54 BST 2025 port directory: /usr/ports/biology/hhsuite package name: hhsuite-3.3.0_3 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1071 Dec 29 14:16 /usr/ports/biology/hhsuite/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: 1a35b19e6d Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 03 ---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/03/.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--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/hhsuite/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/hhsuite/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/hhsuite/work/.cache HOME=/wrkdirs/usr/ports/biology/hhsuite/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/hhsuite/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/hhsuite/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/hhsuite/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/hhsuite/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/hhsuite/work/.cache HOME=/wrkdirs/usr/ports/biology/hhsuite/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/hhsuite/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/hhsuite/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/hhsuite/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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-- OPENMP="" CMAKE_BUILD_TYPE="release" PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=14.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.36.3 PERL_VER=5.36 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.36 DOCSDIR="share/doc/hhsuite" EXAMPLESDIR="share/examples/hhsuite" DATADIR="share/hhsuite" WWWDIR="www/hhsuite" ETCDIR="etc/hhsuite" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/hhsuite DOCSDIR=/usr/local/share/doc/hhsuite EXAMPLESDIR=/usr/local/share/examples/hhsuite WWWDIR=/usr/local/www/hhsuite ETCDIR=/usr/local/etc/hhsuite --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 ===> hhsuite-3.3.0_3 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 ===> hhsuite-3.3.0_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of hhsuite-3.3.0_3 =========================================================================== =================================================== ===== 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 hhsuite-3.3.0_3 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by hhsuite-3.3.0_3 for building => SHA256 Checksum OK for soedinglab-hh-suite-v3.3.0_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 hhsuite-3.3.0_3 for building ===> Extracting for hhsuite-3.3.0_3 => SHA256 Checksum OK for soedinglab-hh-suite-v3.3.0_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 hhsuite-3.3.0_3 ===> Applying FreeBSD patches for hhsuite-3.3.0_3 from /usr/ports/biology/hhsuite/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> hhsuite-3.3.0_3 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 ===> hhsuite-3.3.0_3 depends on file: /usr/local/bin/cmake - found ===> Returning to build of hhsuite-3.3.0_3 ===> hhsuite-3.3.0_3 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 ===> hhsuite-3.3.0_3 depends on executable: ninja - found ===> Returning to build of hhsuite-3.3.0_3 ===> hhsuite-3.3.0_3 depends on file: /usr/local/bin/python3.11 - found ===> hhsuite-3.3.0_3 depends on package: perl5>=5.36<5.37 - not found ===> Installing existing package /packages/All/perl5-5.36.3_3.pkg [pkg-builder.dan.net.uk] Installing perl5-5.36.3_3... [pkg-builder.dan.net.uk] Extracting perl5-5.36.3_3: .......... done ===> hhsuite-3.3.0_3 depends on package: perl5>=5.36<5.37 - found ===> Returning to build of hhsuite-3.3.0_3 ===> hhsuite-3.3.0_3 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. ===> hhsuite-3.3.0_3 depends on file: /usr/local/bin/ccache - found ===> Returning to build of hhsuite-3.3.0_3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> hhsuite-3.3.0_3 depends on shared library: libmpi.so - not found ===> Installing existing package /packages/All/openmpi-5.0.7_1.pkg [pkg-builder.dan.net.uk] Installing openmpi-5.0.7_1... [pkg-builder.dan.net.uk] `-- Installing gcc13-13.3.0_2... [pkg-builder.dan.net.uk] | `-- Installing binutils-2.44,1... [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 binutils-2.44,1: .......... 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-4.2.2,1... [pkg-builder.dan.net.uk] | | `-- Extracting mpfr-4.2.2,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting mpc-1.3.1_1: ...... done [pkg-builder.dan.net.uk] `-- Extracting gcc13-13.3.0_2: .......... 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] `-- Installing hwloc2-2.11.2... [pkg-builder.dan.net.uk] | `-- Installing level-zero-1.21.9... [pkg-builder.dan.net.uk] | | `-- Installing libfmt-10.2.1... [pkg-builder.dan.net.uk] | | `-- Extracting libfmt-10.2.1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing spdlog-1.15.2... [pkg-builder.dan.net.uk] | | `-- Extracting spdlog-1.15.2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting level-zero-1.21.9: .......... done [pkg-builder.dan.net.uk] | `-- Installing libpciaccess-0.18.1_1... [pkg-builder.dan.net.uk] | | `-- Installing hwdata-0.394,1... [pkg-builder.dan.net.uk] | | `-- Extracting hwdata-0.394,1: ...... done [pkg-builder.dan.net.uk] | `-- Extracting libpciaccess-0.18.1_1: ..... done [pkg-builder.dan.net.uk] | `-- Installing libxml2-2.11.9... [pkg-builder.dan.net.uk] | `-- Extracting libxml2-2.11.9: .......... done [pkg-builder.dan.net.uk] `-- Extracting hwloc2-2.11.2: .......... done [pkg-builder.dan.net.uk] `-- Installing libevent-2.1.12... [pkg-builder.dan.net.uk] `-- Extracting libevent-2.1.12: .......... done [pkg-builder.dan.net.uk] `-- Installing munge-0.5.16... [pkg-builder.dan.net.uk] | `-- Installing libgcrypt-1.11.0... [pkg-builder.dan.net.uk] | | `-- Installing libgpg-error-1.55... [pkg-builder.dan.net.uk] | | `-- Extracting libgpg-error-1.55: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libgcrypt-1.11.0: .......... done [pkg-builder.dan.net.uk] `-- Extracting munge-0.5.16: ......... done [pkg-builder.dan.net.uk] Extracting openmpi-5.0.7_1: .......... done ===== Message from gcc13-13.3.0_2: -- 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. ===> hhsuite-3.3.0_3 depends on shared library: libmpi.so - found (/usr/local/mpi/openmpi/lib/libmpi.so) ===> Returning to build of hhsuite-3.3.0_3 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for hhsuite-3.3.0_3 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/hhsuite/work/.build CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- 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 -- Compiler is clang(++) CMake Deprecation Warning at lib/ffindex/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Looking for fmemopen -- Looking for fmemopen - found -- Found MPI_C: /usr/local/mpi/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/local/mpi/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- xxd not found, using xxdi.pl instead -- 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 OpenMP -- Configuring done (2.5s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: BOOST_PYTHON_SUFFIX CMAKE_COLOR_MAKEFILE CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE FETCHCONTENT_FULLY_DISCONNECTED Python3_EXECUTABLE Python_ADDITIONAL_VERSIONS Python_EXECUTABLE THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/biology/hhsuite/work/.build =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for hhsuite-3.3.0_3 [ 0% 1/114] /usr/local/libexec/ccache/cc -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffindex.c [ 1% 2/114] /usr/local/libexec/ccache/cc -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffutil.c [ 2% 3/114] : && /usr/local/bin/cmake -E rm -f lib/ffindex/src/libffindex.a && /usr/bin/llvm-ar qc lib/ffindex/src/libffindex.a lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o && /usr/bin/llvm-ranlib lib/ffindex/src/libffindex.a && : [ 3% 4/114] /usr/local/libexec/ccache/cc -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffindex_apply_mpi.c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffindex_apply_mpi.c:172:106: warning: format specifies type 'long long' but the argument has type 'int64_t' (aka 'long') [-Wformat] 172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); | ~~~~ ^~~~~~~~~~~ | %ld 1 warning generated. 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-L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong -Wl,-rpath=-Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath -Wl,/usr/local/mpi/openmpi/lib -Wl,--enable-new-dtags -pthread -Xlinker --dependency-file=src/CMakeFiles/hhalign_mpi.dir/link.d src/CMakeFiles/hhalign_mpi.dir/hhblits_mpi.cpp.o -o src/hhalign_mpi -Wl,-rpath,/usr/local/mpi/openmpi/lib: src/libHH_OBJECTS.a lib/ffindex/src/mpq/libmpq.a /usr/local/mpi/openmpi/lib/libmpi.so lib/ffindex/src/libffindex.a src/cs/libCS_OBJECTS.a src/libhhviterbialgorithm_with_celloff.a src/libhhviterbialgorithm_and_ss.a src/libhhviterbialgorithm_with_celloff_and_ss.a -lomp && : [100% 114/114] : && /usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -msse2 -fopenmp=libomp -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong -Wl,-rpath=-Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath -Wl,/usr/local/mpi/openmpi/lib -Wl,--enable-new-dtags -pthread -Xlinker --dependency-file=src/CMakeFiles/cstranslate_mpi.dir/link.d src/CMakeFiles/cstranslate_mpi.dir/cs/cstranslate_mpi_app.cc.o -o src/cstranslate_mpi -Wl,-rpath,/usr/local/mpi/openmpi/lib: src/libHH_OBJECTS.a src/libA3M_COMPRESS.a lib/ffindex/src/mpq/libmpq.a /usr/local/mpi/openmpi/lib/libmpi.so lib/ffindex/src/libffindex.a src/cs/libCS_OBJECTS.a src/libhhviterbialgorithm_with_celloff.a src/libhhviterbialgorithm_and_ss.a src/libhhviterbialgorithm_with_celloff_and_ss.a -lomp && : =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> hhsuite-3.3.0_3 depends on file: /usr/local/bin/python3.11 - found ===> hhsuite-3.3.0_3 depends on package: perl5>=5.36<5.37 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for hhsuite-3.3.0_3 ===> Generating temporary packing list [ 0% 1/1] cd /wrkdirs/usr/ports/biology/hhsuite/work/.build && /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/ffindex_apply_mpi -- Set non-toolchain portion of runtime path of "/wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/ffindex_apply_mpi" to "/usr/local/mpi/openmpi/lib" -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/ffindex_reduce -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/ffindex_apply -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/ffindex_build -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/ffindex_from_fasta -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/ffindex_get -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/ffindex_modify -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/ffindex_unpack -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/ffindex_order -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/ffindex_from_fasta_with_split -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/data/context_data.crf -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/data/context_data.lib -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/data/cs219.lib -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/data/do_not_delete -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/data/do_not_delete.phr -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/data/do_not_delete.pin -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/data/do_not_delete.psq -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhblits -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhmake -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhfilter -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhsearch -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhalign -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhconsensus -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/a3m_extract -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/a3m_reduce -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/a3m_database_reduce -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/a3m_database_extract -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/a3m_database_filter -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/cstranslate -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhblits_omp -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhsearch_omp -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhalign_omp -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhblits_ca3m -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhblits_mpi -- Set non-toolchain portion of runtime path of "/wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhblits_mpi" to "/usr/local/mpi/openmpi/lib" -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhsearch_mpi -- Set non-toolchain portion of runtime path of "/wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhsearch_mpi" to "/usr/local/mpi/openmpi/lib" -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhalign_mpi -- Set non-toolchain portion of runtime path of "/wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhalign_mpi" to "/usr/local/mpi/openmpi/lib" -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/cstranslate_mpi -- Set non-toolchain portion of runtime path of "/wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/cstranslate_mpi" to "/usr/local/mpi/openmpi/lib" -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/scripts/a3m.py -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/scripts/addss.pl -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/scripts/Align.pm -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/scripts/check_a3m.py -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/scripts/cif2fasta.py -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/scripts/create_profile_from_hhm.pl -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/scripts/create_profile_from_hmmer.pl -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/scripts/ffindex.py -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/scripts/get_a3m_size.py -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/scripts/hh_reader.py -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/scripts/hhmakemodel.pl -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/scripts/hhmakemodel.py -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/scripts/HHPaths.pm -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/scripts/hhsuitedb.py -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/scripts/mergeali.pl -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/scripts/multithread.pl -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/scripts/pdb2fasta.pl -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/scripts/pdbfilter.pl -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/scripts/pdbfilter.py -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/scripts/reformat.pl -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/scripts/renumberpdb.pl -- Installing: /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/share/hhsuite/scripts/splitfasta.pl ====> 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=2025-05-06T18:14:54+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=1a35b19e6d' '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 hhsuite-3.3.0_3 ===> Building hhsuite-3.3.0_3 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for hhsuite-3.3.0_3 build of biology/hhsuite | hhsuite-3.3.0_3 ended at Tue May 6 19:20:31 BST 2025 build time: 00:05:38