=>> Building biology/py-cutadapt build started at Sat Nov 1 06:27:28 EDT 2025 port directory: /usr/ports/biology/py-cutadapt package name: py311-cutadapt-5.1 building for: FreeBSD pkg.DaveG.ca 14.3-RELEASE-p1 FreeBSD 14.3-RELEASE-p1 1403000 amd64 maintained by: jadawin@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 996 Jun 29 20:14 /usr/ports/biology/py-cutadapt/Makefile Ports top last git commit: 9bb805acfc67 Ports top unclean checkout: no Port dir last git commit: e16761234cdb Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500066 Jail OSVERSION: 1403000 Job Id: 02 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1403000 UNAME_v=FreeBSD 14.3-RELEASE-p1 1403000 UNAME_r=14.3-RELEASE-p1 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/freebsd_14_3_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_14_3_x64-HEAD-ALL/02/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_3_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_3_x64-HEAD-ALL/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=py311 MAKE_ARGS= FLAVOR=py311 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jadawin@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-cutadapt/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-cutadapt/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-cutadapt/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-cutadapt/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-cutadapt/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-cutadapt/work-py311/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-cutadapt/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-cutadapt/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-cutadapt/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-cutadapt/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-cutadapt/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-cutadapt/work-py311/.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 LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " 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-- PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=14.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/py311-cutadapt" EXAMPLESDIR="share/examples/py311-cutadapt" DATADIR="share/py311-cutadapt" WWWDIR="www/py311-cutadapt" ETCDIR="etc/py311-cutadapt" --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_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/py311-cutadapt DOCSDIR=/usr/local/share/doc/py311-cutadapt EXAMPLESDIR=/usr/local/share/examples/py311-cutadapt WWWDIR=/usr/local/www/py311-cutadapt ETCDIR=/usr/local/etc/py311-cutadapt --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 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 #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 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 ===> py311-cutadapt-5.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.3.1_1.pkg [pkg.DaveG.ca] Installing pkg-2.3.1_1... [pkg.DaveG.ca] Extracting pkg-2.3.1_1: .......... done ===> py311-cutadapt-5.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py311-cutadapt-5.1 =========================================================================== =================================================== ===== 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 py311-cutadapt-5.1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py311-cutadapt-5.1 for building => SHA256 Checksum OK for cutadapt-5.1.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 py311-cutadapt-5.1 for building ===> Extracting for py311-cutadapt-5.1 => SHA256 Checksum OK for cutadapt-5.1.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 py311-cutadapt-5.1 ===> Applying FreeBSD patches for py311-cutadapt-5.1 from /usr/ports/biology/py-cutadapt/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-cutadapt-5.1 depends on package: py311-setuptools-scm>0 - not found ===> Installing existing package /packages/All/py311-setuptools-scm-8.0.4_2.pkg [pkg.DaveG.ca] Installing py311-setuptools-scm-8.0.4_2... [pkg.DaveG.ca] `-- Installing py311-packaging-25.0... [pkg.DaveG.ca] | `-- Installing python311-3.11.14... [pkg.DaveG.ca] | | `-- Installing gettext-runtime-0.23.1... [pkg.DaveG.ca] | | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | | `-- Extracting gettext-runtime-0.23.1: .......... done [pkg.DaveG.ca] | | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] | | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | | `-- Installing readline-8.2.13_2... [pkg.DaveG.ca] | | `-- Extracting readline-8.2.13_2: .......... done [pkg.DaveG.ca] | `-- Extracting python311-3.11.14: .......... done [pkg.DaveG.ca] `-- Extracting py311-packaging-25.0: .......... done [pkg.DaveG.ca] `-- Installing py311-setuptools-63.1.0_3... [pkg.DaveG.ca] `-- Extracting py311-setuptools-63.1.0_3: .......... done [pkg.DaveG.ca] `-- Installing py311-typing-extensions-4.15.0... [pkg.DaveG.ca] `-- Extracting py311-typing-extensions-4.15.0: ....... done [pkg.DaveG.ca] Extracting py311-setuptools-scm-8.0.4_2: .......... done ===== Message from python311-3.11.14: -- 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 ===> py311-cutadapt-5.1 depends on package: py311-setuptools-scm>0 - found ===> Returning to build of py311-cutadapt-5.1 ===> py311-cutadapt-5.1 depends on package: py311-cython>=0.29.37<3 - not found ===> Installing existing package /packages/All/py311-cython-0.29.37_2.pkg [pkg.DaveG.ca] Installing py311-cython-0.29.37_2... [pkg.DaveG.ca] Extracting py311-cython-0.29.37_2: .......... done ===> py311-cutadapt-5.1 depends on package: py311-cython>=0.29.37<3 - found ===> Returning to build of py311-cutadapt-5.1 ===> py311-cutadapt-5.1 depends on package: py311-setuptools>=63.1.0 - found ===> py311-cutadapt-5.1 depends on file: /usr/local/bin/python3.11 - found ===> py311-cutadapt-5.1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] 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. ===> py311-cutadapt-5.1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of py311-cutadapt-5.1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for py311-cutadapt-5.1 /usr/local/lib/python3.11/site-packages/setuptools/config/pyprojecttoml.py:104: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*. warnings.warn(msg, _BetaConfiguration) running config =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for py311-cutadapt-5.1 /usr/local/lib/python3.11/site-packages/setuptools/config/pyprojecttoml.py:104: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*. warnings.warn(msg, _BetaConfiguration) running build running build_py creating build creating build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311 creating build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/files.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/steps.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/predicates.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/__main__.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/__init__.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/log.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/modifiers.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/statistics.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/adapters.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/tokenizer.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/json.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/align.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/report.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/pipeline.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/cli.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/parser.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/utils.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/runners.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/_match_tables.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/kmer_heuristic.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/_version.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt running egg_info writing src/cutadapt.egg-info/PKG-INFO writing dependency_links to src/cutadapt.egg-info/dependency_links.txt writing entry points to src/cutadapt.egg-info/entry_points.txt writing requirements to src/cutadapt.egg-info/requires.txt writing top-level names to src/cutadapt.egg-info/top_level.txt reading manifest file 'src/cutadapt.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'src/cutadapt/*.c' adding license file 'LICENSE' writing manifest file 'src/cutadapt.egg-info/SOURCES.txt' copying src/cutadapt/_align.pyi -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/_kmer_finder.pyi -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/info.pyi -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt copying src/cutadapt/qualtrim.pyi -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt running build_ext cythoning src/cutadapt/_align.pyx to src/cutadapt/_align.c cythoning src/cutadapt/qualtrim.pyx to src/cutadapt/qualtrim.c cythoning src/cutadapt/info.pyx to src/cutadapt/info.c /usr/local/lib/python3.11/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/cutadapt-5.1/src/cutadapt/info.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning src/cutadapt/_kmer_finder.pyx to src/cutadapt/_kmer_finder.c building 'cutadapt._align' extension creating build/temp.freebsd-14.3-RELEASE-p1-amd64-cpython-311 creating build/temp.freebsd-14.3-RELEASE-p1-amd64-cpython-311/src creating build/temp.freebsd-14.3-RELEASE-p1-amd64-cpython-311/src/cutadapt cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/include/python3.11 -c src/cutadapt/_align.c -o build/temp.freebsd-14.3-RELEASE-p1-amd64-cpython-311/src/cutadapt/_align.o src/cutadapt/_align.c:11223:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] 11223 | CYTHON_FALLTHROUGH; | ^ src/cutadapt/_align.c:345:34: note: expanded from macro 'CYTHON_FALLTHROUGH' 345 | #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) | ^ src/cutadapt/_align.c:11234:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] 11234 | CYTHON_FALLTHROUGH; | ^ src/cutadapt/_align.c:345:34: note: expanded from macro 'CYTHON_FALLTHROUGH' 345 | #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) | ^ 2 warnings generated. cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.3-RELEASE-p1-amd64-cpython-311/src/cutadapt/_align.o -L/usr/local/lib -o build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/_align.cpython-311.so building 'cutadapt.qualtrim' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/include/python3.11 -c src/cutadapt/qualtrim.c -o build/temp.freebsd-14.3-RELEASE-p1-amd64-cpython-311/src/cutadapt/qualtrim.o cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.3-RELEASE-p1-amd64-cpython-311/src/cutadapt/qualtrim.o -L/usr/local/lib -o build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/qualtrim.cpython-311.so building 'cutadapt.info' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/include/python3.11 -c src/cutadapt/info.c -o build/temp.freebsd-14.3-RELEASE-p1-amd64-cpython-311/src/cutadapt/info.o cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.3-RELEASE-p1-amd64-cpython-311/src/cutadapt/info.o -L/usr/local/lib -o build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/info.cpython-311.so building 'cutadapt._kmer_finder' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/include/python3.11 -c src/cutadapt/_kmer_finder.c -o build/temp.freebsd-14.3-RELEASE-p1-amd64-cpython-311/src/cutadapt/_kmer_finder.o src/cutadapt/_kmer_finder.c:4168:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] 4168 | CYTHON_FALLTHROUGH; | ^ src/cutadapt/_kmer_finder.c:345:34: note: expanded from macro 'CYTHON_FALLTHROUGH' 345 | #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) | ^ src/cutadapt/_kmer_finder.c:4179:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] 4179 | CYTHON_FALLTHROUGH; | ^ src/cutadapt/_kmer_finder.c:345:34: note: expanded from macro 'CYTHON_FALLTHROUGH' 345 | #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) | ^ 2 warnings generated. cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.3-RELEASE-p1-amd64-cpython-311/src/cutadapt/_kmer_finder.o -L/usr/local/lib -o build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/_kmer_finder.cpython-311.so =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-cutadapt-5.1 depends on package: py311-xopen>=1.6.0 - not found ===> Installing existing package /packages/All/py311-xopen-2.0.2.pkg [pkg.DaveG.ca] Installing py311-xopen-2.0.2... [pkg.DaveG.ca] `-- Installing pigz-2.8... [pkg.DaveG.ca] | `-- Installing zopfli-1.0.3_1... [pkg.DaveG.ca] | `-- Extracting zopfli-1.0.3_1: .......... done [pkg.DaveG.ca] `-- Extracting pigz-2.8: ..... done [pkg.DaveG.ca] `-- Installing py311-zstandard-0.23.0_1... [pkg.DaveG.ca] `-- Extracting py311-zstandard-0.23.0_1: .......... done [pkg.DaveG.ca] Extracting py311-xopen-2.0.2: .......... done ===> py311-cutadapt-5.1 depends on package: py311-xopen>=1.6.0 - found ===> Returning to build of py311-cutadapt-5.1 ===> py311-cutadapt-5.1 depends on package: py311-dnaio>=1.2.0 - not found ===> Installing existing package /packages/All/py311-dnaio-1.2.4.pkg [pkg.DaveG.ca] Installing py311-dnaio-1.2.4... [pkg.DaveG.ca] Extracting py311-dnaio-1.2.4: .......... done ===> py311-cutadapt-5.1 depends on package: py311-dnaio>=1.2.0 - found ===> Returning to build of py311-cutadapt-5.1 ===> py311-cutadapt-5.1 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for py311-cutadapt-5.1 ===> Generating temporary packing list /usr/local/lib/python3.11/site-packages/setuptools/config/pyprojecttoml.py:104: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*. warnings.warn(msg, _BetaConfiguration) running install /usr/local/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py copying src/cutadapt/_version.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt running egg_info writing src/cutadapt.egg-info/PKG-INFO writing dependency_links to src/cutadapt.egg-info/dependency_links.txt writing entry points to src/cutadapt.egg-info/entry_points.txt writing requirements to src/cutadapt.egg-info/requires.txt writing top-level names to src/cutadapt.egg-info/top_level.txt reading manifest file 'src/cutadapt.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'src/cutadapt.egg-info/SOURCES.txt' running build_ext skipping 'src/cutadapt/_align.c' Cython extension (up-to-date) skipping 'src/cutadapt/qualtrim.c' Cython extension (up-to-date) skipping 'src/cutadapt/info.c' Cython extension (up-to-date) skipping 'src/cutadapt/_kmer_finder.c' Cython extension (up-to-date) running install_lib creating /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11 creating /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages creating /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/qualtrim.pyi -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/info.pyi -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/files.py -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/steps.py -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/_kmer_finder.pyi -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/predicates.py -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/__main__.py -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/__init__.py -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/_align.pyi -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/log.py -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/_align.cpython-311.so -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/modifiers.py -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/statistics.py -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/adapters.py -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/tokenizer.py -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/json.py -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/align.py -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/info.cpython-311.so -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/qualtrim.cpython-311.so -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/report.py -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/pipeline.py -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/cli.py -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/_kmer_finder.cpython-311.so -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/parser.py -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/utils.py -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/runners.py -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/_match_tables.py -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/kmer_heuristic.py -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/cutadapt/_version.py -> /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt byte-compiling /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt/files.py to files.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt/steps.py to steps.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt/predicates.py to predicates.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt/__main__.py to __main__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt/log.py to log.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt/modifiers.py to modifiers.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt/statistics.py to statistics.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt/adapters.py to adapters.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt/tokenizer.py to tokenizer.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt/json.py to json.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt/align.py to align.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt/report.py to report.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt/pipeline.py to pipeline.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt/cli.py to cli.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt/parser.py to parser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt/utils.py to utils.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt/runners.py to runners.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt/_match_tables.py to _match_tables.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt/kmer_heuristic.py to kmer_heuristic.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt/_version.py to _version.cpython-311.pyc writing byte-compilation script '/tmp/tmpgbznk5_d.py' /usr/local/bin/python3.11 /tmp/tmpgbznk5_d.py removing /tmp/tmpgbznk5_d.py running install_egg_info Copying src/cutadapt.egg-info to /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/lib/python3.11/site-packages/cutadapt-5.1-py3.11.egg-info running install_scripts Installing cutadapt script to /wrkdirs/usr/ports/biology/py-cutadapt/work-py311/stage/usr/local/bin writing list of installed files to '/wrkdirs/usr/ports/biology/py-cutadapt/work-py311/.PLIST.pymodtmp' ===> Creating unique files: Move MAN files needing SUFFIX ===> Creating unique files: Move files needing SUFFIX Move: bin/cutadapt --> bin/cutadapt-3.11 Link: @bin/cutadapt --> bin/cutadapt-3.11 ====> 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=2025-11-01T10:27:28+0000' 'PKG_NOTE_ports_top_git_hash=9bb805acfc67' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=e16761234cdb' '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 py311-cutadapt-5.1 ===> Building py311-cutadapt-5.1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py311-cutadapt-5.1 build of biology/py-cutadapt@py311 | py311-cutadapt-5.1 ended at Sat Nov 1 06:29:48 EDT 2025 build time: 00:02:28