=>> Building biology/python-nexus build started at Sun Jul 12 11:02:36 JST 2026 port directory: /usr/ports/biology/python-nexus package name: py312-python-nexus-2.9.0_1 building for: FreeBSD s15amd64-setuptools2-job-03 15.1-STABLE FreeBSD 15.1-STABLE 1501501 amd64 maintained by: wen@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 620 Apr 13 23:05 /usr/ports/biology/python-nexus/Makefile Ports top last git commit: 9d0203aad0254f4adb0e81c242ad6ec8717647a5 Ports top unclean checkout: yes Port dir last git commit: 1c3394560c4f3b7e3e79480f17b767e3a58bd951 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.8 Host OSVERSION: 1501501 Jail OSVERSION: 1501501 Job Id: 03 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1501501 UNAME_v=FreeBSD 15.1-STABLE 1501501 UNAME_r=15.1-STABLE 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 MASTERMNT=/usr/local/poudriere/data/.m/s15amd64-setuptools2/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color GID=0 OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 UID=0 PWD=/usr/local/poudriere/data/.m/s15amd64-setuptools2/03/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=s15amd64-setuptools2 SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/s15amd64-setuptools2/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.8 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py312 MAKE_ARGS= FLAVOR=py312 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- wen@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.12" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/python-nexus/work-py312 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/python-nexus/work-py312 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/python-nexus/work-py312/.cache HOME=/wrkdirs/usr/ports/biology/python-nexus/work-py312 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/python-nexus/work-py312/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/python-nexus/work-py312/.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/python-nexus/work-py312 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/python-nexus/work-py312 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/python-nexus/work-py312/.cache HOME=/wrkdirs/usr/ports/biology/python-nexus/work-py312 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/python-nexus/work-py312/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/python-nexus/work-py312/.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/python3.12 PYTHON_LIBDIR=lib/python3.12 PYTHON_PLATFORM=freebsd15 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=15.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/python-nexus" EXAMPLESDIR="share/examples/python-nexus" DATADIR="share/python-nexus" WWWDIR="www/python-nexus" ETCDIR="etc/python-nexus" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.12 PYTHON_LIBDIR=/usr/local/lib/python3.12 PYTHON_PLATFORM=freebsd15 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/python-nexus DOCSDIR=/usr/local/share/doc/python-nexus EXAMPLESDIR=/usr/local/share/examples/python-nexus WWWDIR=/usr/local/www/python-nexus ETCDIR=/usr/local/etc/python-nexus --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles OVERLAYS+=/overlays/overlay_setuptools FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### LICENSES_ACCEPTED= EULA ISC MPEG2ENC DEFAULT_VERSIONS+= magick=7 DEFAULT_VERSIONS+= pgsql=18 DEFAULT_VERSIONS+= samba=4.23 DEFAULT_VERSIONS+= ssl=openssl japanese_fcitx5-mozc_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_UNSET= JAWIKI x11_wm_hikari_SET= INPUTMETHOD GAMMA LAYERSHELL SCREENCOPY VIRTUALINPUT X11 .if $(.CURDIR:M*/x11-wm/hikari) WITH_DEBUG= YES .endif #### #### DEFAULT_VERSIONS+= ssl=base devel_gamin_set= LIBINOTIFY #### Misc Poudriere #### .include "/etc/make.conf.ports_env" 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 (kbytes, -y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> License BSD3CLAUSE accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py312-python-nexus-2.9.0_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.7.5.pkg [s15amd64-setuptools2-job-03] Installing pkg-2.7.5... [s15amd64-setuptools2-job-03] Extracting pkg-2.7.5: .......... done ===> py312-python-nexus-2.9.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py312-python-nexus-2.9.0_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py312-python-nexus-2.9.0_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py312-python-nexus-2.9.0_1 for building => SHA256 Checksum OK for python-nexus-2.9.0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py312-python-nexus-2.9.0_1 for building ===> Extracting for py312-python-nexus-2.9.0_1 => SHA256 Checksum OK for python-nexus-2.9.0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Patching for py312-python-nexus-2.9.0_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py312-python-nexus-2.9.0_1 depends on package: py312-setuptools>=63.1.0 - not found ===> Installing existing package /packages/All/py312-setuptools-81.0.0.pkg [s15amd64-setuptools2-job-03] Installing py312-setuptools-81.0.0... [s15amd64-setuptools2-job-03] `-- Installing py312-more-itertools-11.1.0... [s15amd64-setuptools2-job-03] | `-- Installing python312-3.12.13_3... [s15amd64-setuptools2-job-03] | | `-- Installing expat-2.8.2... [s15amd64-setuptools2-job-03] | | `-- Extracting expat-2.8.2: .......... done [s15amd64-setuptools2-job-03] | | `-- Installing gettext-runtime-1.0_1... [s15amd64-setuptools2-job-03] | | `-- Installing indexinfo-0.3.1_1... [s15amd64-setuptools2-job-03] | | `-- Extracting indexinfo-0.3.1_1: .... done [s15amd64-setuptools2-job-03] | | `-- Extracting gettext-runtime-1.0_1: .......... done [s15amd64-setuptools2-job-03] | | `-- Installing libffi-3.6.0... [s15amd64-setuptools2-job-03] | | `-- Extracting libffi-3.6.0: .......... done [s15amd64-setuptools2-job-03] | | `-- Installing mpdecimal-4.0.1... [s15amd64-setuptools2-job-03] | | `-- Extracting mpdecimal-4.0.1: .......... done [s15amd64-setuptools2-job-03] | | `-- Installing openssl-3.0.21,1... [s15amd64-setuptools2-job-03] | | `-- Extracting openssl-3.0.21,1: .......... done [s15amd64-setuptools2-job-03] | | `-- Installing readline-8.3.3... [s15amd64-setuptools2-job-03] | | `-- Extracting readline-8.3.3: .......... done [s15amd64-setuptools2-job-03] | `-- Extracting python312-3.12.13_3: .......... done [s15amd64-setuptools2-job-03] `-- Extracting py312-more-itertools-11.1.0: .......... done [s15amd64-setuptools2-job-03] `-- Installing py312-packaging-26.2... [s15amd64-setuptools2-job-03] `-- Extracting py312-packaging-26.2: .......... done [s15amd64-setuptools2-job-03] `-- Installing py312-wheel-0.47.0... [s15amd64-setuptools2-job-03] `-- Extracting py312-wheel-0.47.0: .......... done [s15amd64-setuptools2-job-03] Extracting py312-setuptools-81.0.0: .......... done ===== Message from openssl-3.0.21,1: -- This port (security/openssl) will update from 3.0 to 3.5 per 2026-07-01 (2026Q3) in anticipation of the End-of-Life of OpenSSL 3.0. A new port (security/openssl30) will be created for the remainder of the lifespan of OpenSSL 3.0 and FreeBSD 14. See: https://openssl-library.org/roadmap/index.html ===== Message from python312-3.12.13_3: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py312-gdbm databases/py-gdbm@py312 py312-sqlite3 databases/py-sqlite3@py312 py312-tkinter x11-toolkits/py-tkinter@py312 ===> py312-python-nexus-2.9.0_1 depends on package: py312-setuptools>=63.1.0 - found ===> Returning to build of py312-python-nexus-2.9.0_1 ===> py312-python-nexus-2.9.0_1 depends on file: /usr/local/bin/python3.12 - found =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Configuring for py312-python-nexus-2.9.0_1 /usr/local/lib/python3.12/site-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: BSD License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running config =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building for py312-python-nexus-2.9.0_1 /usr/local/lib/python3.12/site-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: BSD License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running build running build_py creating build/lib/nexus copying src/nexus/writer.py -> build/lib/nexus copying src/nexus/cli_util.py -> build/lib/nexus copying src/nexus/reader.py -> build/lib/nexus copying src/nexus/__main__.py -> build/lib/nexus copying src/nexus/__init__.py -> build/lib/nexus copying src/nexus/util.py -> build/lib/nexus copying src/nexus/exceptions.py -> build/lib/nexus copying src/nexus/checker.py -> build/lib/nexus creating build/lib/nexus/handlers copying src/nexus/handlers/tree.py -> build/lib/nexus/handlers copying src/nexus/handlers/__init__.py -> build/lib/nexus/handlers copying src/nexus/handlers/taxa.py -> build/lib/nexus/handlers copying src/nexus/handlers/data.py -> build/lib/nexus/handlers creating build/lib/nexus/commands copying src/nexus/commands/describetaxa.py -> build/lib/nexus/commands copying src/nexus/commands/tally.py -> build/lib/nexus/commands copying src/nexus/commands/combine.py -> build/lib/nexus/commands copying src/nexus/commands/deinterleave.py -> build/lib/nexus/commands copying src/nexus/commands/__init__.py -> build/lib/nexus/commands copying src/nexus/commands/randomise.py -> build/lib/nexus/commands copying src/nexus/commands/edit.py -> build/lib/nexus/commands copying src/nexus/commands/binary2multistate.py -> build/lib/nexus/commands copying src/nexus/commands/check.py -> build/lib/nexus/commands copying src/nexus/commands/multistate2binary.py -> build/lib/nexus/commands copying src/nexus/commands/convert.py -> build/lib/nexus/commands copying src/nexus/commands/describecharacter.py -> build/lib/nexus/commands copying src/nexus/commands/trees.py -> build/lib/nexus/commands creating build/lib/nexus/tools copying src/nexus/tools/binarise.py -> build/lib/nexus/tools copying src/nexus/tools/__init__.py -> build/lib/nexus/tools copying src/nexus/tools/shufflenexus.py -> build/lib/nexus/tools copying src/nexus/tools/combine_nexuses.py -> build/lib/nexus/tools copying src/nexus/tools/check_zeros.py -> build/lib/nexus/tools copying src/nexus/tools/util.py -> build/lib/nexus/tools copying src/nexus/tools/multistatise.py -> build/lib/nexus/tools copying src/nexus/tools/sites.py -> build/lib/nexus/tools copying src/nexus/tools/trees.py -> build/lib/nexus/tools =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py312-python-nexus-2.9.0_1 depends on package: py312-clldutils>=0 - not found ===> Installing existing package /packages/All/py312-clldutils-3.24.2_2.pkg [s15amd64-setuptools2-job-03] Installing py312-clldutils-3.24.2_2... [s15amd64-setuptools2-job-03] `-- Installing py312-attrs-26.1.0... [s15amd64-setuptools2-job-03] `-- Extracting py312-attrs-26.1.0: .......... done [s15amd64-setuptools2-job-03] `-- Installing py312-colorlog-6.10.1... [s15amd64-setuptools2-job-03] `-- Extracting py312-colorlog-6.10.1: .......... done [s15amd64-setuptools2-job-03] `-- Installing py312-lxml-6.1.1... [s15amd64-setuptools2-job-03] | `-- Installing libxml2-2.15.3... [s15amd64-setuptools2-job-03] | `-- Extracting libxml2-2.15.3: .......... done [s15amd64-setuptools2-job-03] | `-- Installing libxslt-1.1.45... [s15amd64-setuptools2-job-03] | | `-- Installing libgcrypt-1.12.2... [s15amd64-setuptools2-job-03] | | `-- Installing libgpg-error-1.61... [s15amd64-setuptools2-job-03] | | `-- Extracting libgpg-error-1.61: .......... done [s15amd64-setuptools2-job-03] | | `-- Extracting libgcrypt-1.12.2: .......... done [s15amd64-setuptools2-job-03] | `-- Extracting libxslt-1.1.45: .......... done [s15amd64-setuptools2-job-03] `-- Extracting py312-lxml-6.1.1: .......... done [s15amd64-setuptools2-job-03] `-- Installing py312-markdown-3.10.2... [s15amd64-setuptools2-job-03] `-- Extracting py312-markdown-3.10.2: .......... done [s15amd64-setuptools2-job-03] `-- Installing py312-markupsafe-3.0.3... [s15amd64-setuptools2-job-03] `-- Extracting py312-markupsafe-3.0.3: .......... done [s15amd64-setuptools2-job-03] `-- Installing py312-python-dateutil-2.9.0... [s15amd64-setuptools2-job-03] | `-- Installing py312-six-1.17.0... [s15amd64-setuptools2-job-03] | `-- Extracting py312-six-1.17.0: .......... done [s15amd64-setuptools2-job-03] `-- Extracting py312-python-dateutil-2.9.0: .......... done [s15amd64-setuptools2-job-03] `-- Installing py312-tabulate-0.10.0... [s15amd64-setuptools2-job-03] | `-- Installing py312-wcwidth-0.8.2... [s15amd64-setuptools2-job-03] | `-- Extracting py312-wcwidth-0.8.2: .......... done [s15amd64-setuptools2-job-03] `-- Extracting py312-tabulate-0.10.0: .......... done [s15amd64-setuptools2-job-03] Extracting py312-clldutils-3.24.2_2: .......... done ===> py312-python-nexus-2.9.0_1 depends on package: py312-clldutils>=0 - found ===> Returning to build of py312-python-nexus-2.9.0_1 ===> py312-python-nexus-2.9.0_1 depends on package: py312-termcolor>=0 - not found ===> Installing existing package /packages/All/py312-termcolor-3.3.0.pkg [s15amd64-setuptools2-job-03] Installing py312-termcolor-3.3.0... [s15amd64-setuptools2-job-03] Extracting py312-termcolor-3.3.0: .......... done ===> py312-python-nexus-2.9.0_1 depends on package: py312-termcolor>=0 - found ===> Returning to build of py312-python-nexus-2.9.0_1 ===> py312-python-nexus-2.9.0_1 depends on package: py312-newick>=0 - not found ===> Installing existing package /packages/All/py312-newick-1.11.0.pkg [s15amd64-setuptools2-job-03] Installing py312-newick-1.11.0... [s15amd64-setuptools2-job-03] Extracting py312-newick-1.11.0: .......... done ===> py312-python-nexus-2.9.0_1 depends on package: py312-newick>=0 - found ===> Returning to build of py312-python-nexus-2.9.0_1 ===> py312-python-nexus-2.9.0_1 depends on file: /usr/local/bin/python3.12 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Staging for py312-python-nexus-2.9.0_1 ===> Generating temporary packing list /usr/local/lib/python3.12/site-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: BSD License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running install /usr/local/lib/python3.12/site-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running install_lib creating /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages creating /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus copying build/lib/nexus/writer.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus copying build/lib/nexus/cli_util.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus copying build/lib/nexus/reader.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus copying build/lib/nexus/__main__.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus copying build/lib/nexus/__init__.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus creating /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/handlers copying build/lib/nexus/handlers/tree.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/handlers copying build/lib/nexus/handlers/__init__.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/handlers copying build/lib/nexus/handlers/taxa.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/handlers copying build/lib/nexus/handlers/data.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/handlers creating /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands copying build/lib/nexus/commands/describetaxa.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands copying build/lib/nexus/commands/tally.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands copying build/lib/nexus/commands/combine.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands copying build/lib/nexus/commands/deinterleave.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands copying build/lib/nexus/commands/__init__.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands copying build/lib/nexus/commands/randomise.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands copying build/lib/nexus/commands/edit.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands copying build/lib/nexus/commands/binary2multistate.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands copying build/lib/nexus/commands/check.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands copying build/lib/nexus/commands/multistate2binary.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands copying build/lib/nexus/commands/convert.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands copying build/lib/nexus/commands/describecharacter.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands copying build/lib/nexus/commands/trees.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands copying build/lib/nexus/util.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus creating /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/tools copying build/lib/nexus/tools/binarise.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/tools copying build/lib/nexus/tools/__init__.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/tools copying build/lib/nexus/tools/shufflenexus.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/tools copying build/lib/nexus/tools/combine_nexuses.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/tools copying build/lib/nexus/tools/check_zeros.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/tools copying build/lib/nexus/tools/util.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/tools copying build/lib/nexus/tools/multistatise.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/tools copying build/lib/nexus/tools/sites.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/tools copying build/lib/nexus/tools/trees.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/tools copying build/lib/nexus/exceptions.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus copying build/lib/nexus/checker.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/writer.py to writer.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/cli_util.py to cli_util.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/reader.py to reader.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/__main__.py to __main__.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/__init__.py to __init__.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/handlers/tree.py to tree.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/handlers/__init__.py to __init__.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/handlers/taxa.py to taxa.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/handlers/data.py to data.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands/describetaxa.py to describetaxa.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands/tally.py to tally.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands/combine.py to combine.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands/deinterleave.py to deinterleave.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands/__init__.py to __init__.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands/randomise.py to randomise.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands/edit.py to edit.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands/binary2multistate.py to binary2multistate.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands/check.py to check.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands/multistate2binary.py to multistate2binary.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands/convert.py to convert.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands/describecharacter.py to describecharacter.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/commands/trees.py to trees.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/util.py to util.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/tools/binarise.py to binarise.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/tools/__init__.py to __init__.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/tools/shufflenexus.py to shufflenexus.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/tools/combine_nexuses.py to combine_nexuses.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/tools/check_zeros.py to check_zeros.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/tools/util.py to util.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/tools/multistatise.py to multistatise.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/tools/sites.py to sites.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/tools/trees.py to trees.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/exceptions.py to exceptions.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/nexus/checker.py to checker.cpython-312.pyc writing byte-compilation script '/tmp/tmpkvv5s5yz.py' /usr/local/bin/python3.12 /tmp/tmpkvv5s5yz.py removing /tmp/tmpkvv5s5yz.py running install_egg_info running egg_info writing src/python_nexus.egg-info/PKG-INFO writing dependency_links to src/python_nexus.egg-info/dependency_links.txt writing entry points to src/python_nexus.egg-info/entry_points.txt writing requirements to src/python_nexus.egg-info/requires.txt writing top-level names to src/python_nexus.egg-info/top_level.txt reading manifest file 'src/python_nexus.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '*.py[co]' found anywhere in distribution adding license file 'LICENSE' writing manifest file 'src/python_nexus.egg-info/SOURCES.txt' Copying src/python_nexus.egg-info to /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/lib/python3.12/site-packages/python_nexus-2.9.0-py3.12.egg-info running install_scripts Installing nexus script to /wrkdirs/usr/ports/biology/python-nexus/work-py312/stage/usr/local/bin writing list of installed files to '/wrkdirs/usr/ports/biology/python-nexus/work-py312/.PLIST.pymodtmp' ====> 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=2026-07-12T02:02:36+0000' 'PKG_NOTE_ports_top_git_hash=9d0203aad0254f4adb0e81c242ad6ec8717647a5' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=1c3394560c4f3b7e3e79480f17b767e3a58bd951' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.8' NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building packages for py312-python-nexus-2.9.0_1 ===> Building py312-python-nexus-2.9.0_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py312-python-nexus-2.9.0_1 build of biology/python-nexus@py312 | py312-python-nexus-2.9.0_1 ended at Sun Jul 12 11:05:06 JST 2026 build time: 00:02:51