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Maintainer: [email protected] Log URL: https://pkg-status.freebsd.org/beefy22/data/144amd64-default/c15851b5d6fc/logs/hhsuite-3.3.0_3.log Build URL: https://pkg-status.freebsd.org/beefy22/build.html?mastername=144amd64-default&build=c15851b5d6fc Log: =>> Building biology/hhsuite build started at Sat Aug 29 19:29:54 UTC 2026 port directory: /usr/ports/biology/hhsuite package name: hhsuite-3.3.0_3 building for: FreeBSD 144amd64-default-job-21 14.4-RELEASE-p9 FreeBSD 14.4-RELEASE-p9 amd64 maintained by: [email protected] Makefile datestamp: -rw-r--r-- 1 root wheel 1066 May 9 01:01 /usr/ports/biology/hhsuite/Makefile Ports top last git commit: c15851b5d6fc3781f592602edc35589c21774938 Ports top unclean checkout: no Port dir last git commit: 2a7c0561200c6cf9d0c0252cd4a7ab446eca8e4a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.8-2-g2e891d4a Host OSVERSION: 1600019 Jail OSVERSION: 1404000 Job Id: 21 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1404000 UNAME_v=FreeBSD 14.4-RELEASE-p9 UNAME_r=14.4-RELEASE-p9 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=3.4.8-2-g2e891d4a MASTERMNT=/usr/local/poudriere/data/.m/144amd64-default/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/144amd64-default/21/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=144amd64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/144amd64-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.8-2-g2e891d4a 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-- [email protected] --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/python3.12" 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 " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_I NSTALL_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/python3.12 PYTHON_LIBDIR=lib/python3.12 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.12/site-packages PYTHON_SUFFIX=312 PYTHON_BASESUFFIX=312 PYTHON_TAG=.cpython-312 PYTHON_SOABI=.cpython-312 PYTHON_VER=3.12 PYTHON_BASEVER=3.12 PYTHON_VERSION=python3.12 PYTHON2="@comment " PYTHON3="" OSREL=14.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.42.3 PERL_VER=5.42 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/5.42 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/python3.12 PYTHON_LIBDIR=/usr/local/lib/python3.12 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.12/site-packages PYTHON_SUFFIX=312 PYTHON_BASESUFFIX=312 PYTHON_TAG=.cpython-312 PYTHON_SOABI=.cpython-312 PYTHON_VER=3.12 PYTHON_BASEVER=3.12 PYTHON_VERSION=python3.12 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 PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # 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 3 jobs MAKE_JOBS_NUMBER=3 #### 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-- =======================<phase: check-sanity >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== 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-2.8.4.pkg [144amd64-default-job-21] Installing pkg-2.8.4... [144amd64-default-job-21] Extracting pkg-2.8.4: .......... done ===> hhsuite-3.3.0_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of hhsuite-3.3.0_3 =========================================================================== =======================<phase: fetch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: fetch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by hhsuite-3.3.0_3 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user ===> 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. =========================================================================== =======================<phase: extract-depends>============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: extract >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user ===> 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. =========================================================================== =======================<phase: patch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: patch >============================ ===== 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 =========================================================================== =======================<phase: build-depends >============================ ===== 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-3.31.12_3.pkg [144amd64-default-job-21] Installing cmake-core-3.31.12_3... [144amd64-default-job-21] `-- Installing expat-2.8.3... [144amd64-default-job-21] `-- Extracting expat-2.8.3: .......... done [144amd64-default-job-21] `-- Installing jsoncpp-1.9.6_1... [144amd64-default-job-21] `-- Extracting jsoncpp-1.9.6_1: .......... done [144amd64-default-job-21] `-- Installing libidn2-2.3.8... [144amd64-default-job-21] | `-- Installing indexinfo-0.3.1_1... [144amd64-default-job-21] | `-- Extracting indexinfo-0.3.1_1: .... done [144amd64-default-job-21] | `-- Installing libunistring-1.4.2... [144amd64-default-job-21] | `-- Extracting libunistring-1.4.2: .......... done [144amd64-default-job-21] `-- Extracting libidn2-2.3.8: .......... done [144amd64-default-job-21] `-- Installing libuv-1.52.1... [144amd64-default-job-21] `-- Extracting libuv-1.52.1: .......... done [144amd64-default-job-21] `-- Installing rhash-1.4.6... [144amd64-default-job-21] | `-- Installing gettext-runtime-1.0_1... [144amd64-default-job-21] | `-- Extracting gettext-runtime-1.0_1: .......... done [144amd64-default-job-21] `-- Extracting rhash-1.4.6: .......... done [144amd64-default-job-21] Extracting cmake-core-3.31.12_3: .......... 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-1.13.2,4.pkg <snip> [ 1% 2/102] /usr/bin/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% 3/102] cd /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/data && mkdir -p /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated && /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/cmake/xxdi.pl context_data.crf > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.crf.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.crf.h > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.crf.h.tmp && mv -f /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.crf.h.tmp /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.crf.h [ 3% 4/102] cd /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/data && mkdir -p /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated && /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/cmake/xxdi.pl context_data.lib > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.lib.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.lib.h > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.lib.h.tmp && mv -f /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.lib.h.tmp /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.lib.h [ 4% 5/102] cd /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/data && mkdir -p /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated && /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/cmake/xxdi.pl cs219.lib > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/cs219.lib.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/cs219.lib.h > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/cs219.lib.h.tmp && mv -f /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/cs219.lib.h.tmp /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/cs219.lib.h [ 5% 6/102] /usr/bin/c++ -DOPENMP -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/.build/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs -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 -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3 .3.0/src/hhviterbialgorithm.cpp [ 6% 7/102] /usr/bin/c++ -DOPENMP -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/.build/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs -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 -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /wrkdirs /usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/hhviterbialgorithm.cpp [ 7% 8/102] /usr/bin/c++ -DOPENMP -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/.build/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs -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 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/hhviterb ialgorithm.cpp [ 8% 9/102] /usr/bin/c++ -DOPENMP -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/.build/src -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -msse2 -fopenmp=libomp -fno-strict-aliasing -O2 -pipe 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src/libhhviterbialgorithm_with_celloff_and_ss.a -lomp && : [ 86% 88/102] : && /usr/bin/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 -Xlinker --dependency-file=src/CMakeFiles/hhmake.dir/link.d src/CMakeFiles/hhmake.dir/hhmake.cpp.o -o src/hhmake src/libHH_OBJECTS.a 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 && : [ 87% 89/102] : && /usr/bin/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 -Xlinker --dependency-file=src/CMakeFiles/hhfilter.dir/link.d src/CMakeFiles/hhfilter.dir/hhfilter.cpp.o -o src/hhfilter src/libHH_OBJECTS.a 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 && : [ 88% 90/102] : && /usr/bin/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 -Xlinker --dependency-file=src/CMakeFiles/hhsearch.dir/link.d src/CMakeFiles/hhsearch.dir/hhblits_app.cpp.o -o src/hhsearch src/libHH_OBJECTS.a 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 && : [ 89% 91/102] : && /usr/bin/c++ -O2 -pipe 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src/hhconsensus src/libHH_OBJECTS.a 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 && : [ 91% 93/102] : && /usr/bin/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 -Xlinker --dependency-file=src/CMakeFiles/a3m_extract.dir/link.d src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -o src/a3m_extract lib/ffindex/src/libffindex.a src/libA3M_COMPRESS.a -lomp && : [ 92% 94/102] : && /usr/bin/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 -Xlinker --dependency-file=src/CMakeFiles/a3m_reduce.dir/link.d src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -o src/a3m_reduce lib/ffindex/src/libffindex.a src/libA3M_COMPRESS.a -lomp && : [ 93% 95/102] : && /usr/bin/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 -Xlinker --dependency-file=src/CMakeFiles/a3m_database_reduce.dir/link.d src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -o src/a3m_database_reduce lib/ffindex/src/libffindex.a src/libA3M_COMPRESS.a -lomp && : [ 94% 96/102] : && /usr/bin/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 -Xlinker --dependency-file=src/CMakeFiles/a3m_database_extract.dir/link.d src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -o src/a3m_database_extract lib/ffindex/src/libffindex.a src/libA3M_COMPRESS.a -lomp && : [ 95% 97/102] : && /usr/bin/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 -Xlinker --dependency-file=src/CMakeFiles/a3m_database_filter.dir/link.d src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -o src/a3m_database_filter lib/ffindex/src/libffindex.a src/libA3M_COMPRESS.a -lomp && : [ 96% 98/102] : && /usr/bin/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 -Xlinker --dependency-file=src/CMakeFiles/cstranslate.dir/link.d src/CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -o src/cstranslate src/libHH_OBJECTS.a src/libA3M_COMPRESS.a 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 && : [ 97% 99/102] : && /usr/bin/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 -Xlinker --dependency-file=src/CMakeFiles/hhblits_omp.dir/link.d src/CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -o src/hhblits_omp src/libHH_OBJECTS.a 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 && : [ 98% 100/102] : && /usr/bin/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 -Xlinker --dependency-file=src/CMakeFiles/hhsearch_omp.dir/link.d src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -o src/hhsearch_omp src/libHH_OBJECTS.a 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 && : [ 99% 101/102] : && /usr/bin/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 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src/libhhviterbialgorithm_with_celloff_and_ss.a -lomp && : =========================================================================== =======================<phase: run-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> hhsuite-3.3.0_3 depends on file: /usr/local/bin/python3.12 - found ===> hhsuite-3.3.0_3 depends on package: perl5>=5.42.r<5.43 - found =========================================================================== =======================<phase: stage >============================ ===== 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_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/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) =========================================================================== =======================<phase: package >============================ ===== 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=2026-08-29T19:29:54+0000' 'PKG_NOTE_ports_top_git_hash=c15851b5d6fc3781f592602edc35589c21774938' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=2a7c0561200c6cf9d0c0252cd4a7ab446eca8e4a' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.8-2-g2e891d4a' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for hhsuite-3.3.0_3 ===> Building hhsuite-3.3.0_3 pkg-static: Unable to access file /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/cstranslate_mpi:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/ffindex_apply_mpi:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhalign_mpi:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhblits_mpi:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhsearch_mpi:No such file or directory *** Error code 1 Stop. make: stopped making "package" in /usr/ports/biology/hhsuite
