=>> Building biology/python-nexus build started at Fri Jun 5 20:43:28 JST 2026 port directory: /usr/ports/biology/python-nexus package name: py311-python-nexus-2.9.0_1 building for: FreeBSD curamd64-setuptools-job-01 16.0-CURRENT FreeBSD 16.0-CURRENT 1600018 amd64 maintained by: wen@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 620 May 2 10:17 /usr/ports/biology/python-nexus/Makefile Ports top last git commit: a8b187544 Ports top unclean checkout: yes Port dir last git commit: a8b187544 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.4 Host OSVERSION: 1600018 Jail OSVERSION: 1600018 Job Id: 01 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1600018 UNAME_v=FreeBSD 16.0-CURRENT 1600018 UNAME_r=16.0-CURRENT 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=3.4.4 MASTERMNT=/usr/local/poudriere/data/.m/curamd64-setuptools/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/curamd64-setuptools/01/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=curamd64-setuptools SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/curamd64-setuptools/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.4 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-- wen@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/python-nexus/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/python-nexus/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/python-nexus/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/python-nexus/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/python-nexus/work-py311/.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-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/python-nexus/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/python-nexus/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/python-nexus/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/python-nexus/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/python-nexus/work-py311/.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-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=freebsd16 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=16.0 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/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd16 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/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--- DEFAULT_VERSIONS+= magick=7-x11 DEFAULT_VERSIONS+= pgsql=18 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= GAMMA INPUTMETHOD LAYERSHELL SCREENCOPY VIRTUALINPUT X11 .if $(.CURDIR:M*/x11-wm/hikari) WITH_DEBUG= YES .endif 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+= magick=7-x11 DEFAULT_VERSIONS+= pgsql=18 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= GAMMA INPUTMETHOD LAYERSHELL SCREENCOPY VIRTUALINPUT X11 .if $(.CURDIR:M*/x11-wm/hikari) WITH_DEBUG= YES .endif #### 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) 12099 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=nobody UID=65534 GID=65534 ===> License BSD3CLAUSE accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-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 [curamd64-setuptools-job-01] Installing pkg-2.7.5... [curamd64-setuptools-job-01] Extracting pkg-2.7.5: .......... done ===> py311-python-nexus-2.9.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py311-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 => python-nexus-2.9.0.tar.gz doesn't seem to exist in /portdistfiles. => Attempting to fetch https://files.pythonhosted.org/packages/source/p/python-nexus/python-nexus-2.9.0.tar.gz python-nexus-2.9.0.tar.gz 33 kB 43 MBps 00s ===> Fetching all distfiles required by py311-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 py311-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 py311-python-nexus-2.9.0_1 for building ===> Extracting for py311-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 py311-python-nexus-2.9.0_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-python-nexus-2.9.0_1 depends on package: py311-setuptools>=63.1.0 - not found ===> Installing existing package /packages/All/py311-setuptools-81.0.0.pkg [curamd64-setuptools-job-01] Installing py311-setuptools-81.0.0... [curamd64-setuptools-job-01] `-- Installing py311-more-itertools-10.6.0... [curamd64-setuptools-job-01] | `-- Installing python311-3.11.15_2... [curamd64-setuptools-job-01] | | `-- Installing gettext-runtime-1.0... [curamd64-setuptools-job-01] | | `-- Installing indexinfo-0.3.1_1... [curamd64-setuptools-job-01] | | `-- Extracting indexinfo-0.3.1_1: .... done [curamd64-setuptools-job-01] | | `-- Extracting gettext-runtime-1.0: .......... done [curamd64-setuptools-job-01] | | `-- Installing libffi-3.5.1... [curamd64-setuptools-job-01] | | `-- Extracting libffi-3.5.1: .......... done [curamd64-setuptools-job-01] | | `-- Installing mpdecimal-4.0.1... [curamd64-setuptools-job-01] | | `-- Extracting mpdecimal-4.0.1: .......... done [curamd64-setuptools-job-01] | | `-- Installing openssl-3.0.20,1... [curamd64-setuptools-job-01] | | `-- Extracting openssl-3.0.20,1: .......... done [curamd64-setuptools-job-01] | | `-- Installing readline-8.3.3... [curamd64-setuptools-job-01] | | `-- Extracting readline-8.3.3: .......... done [curamd64-setuptools-job-01] | `-- Extracting python311-3.11.15_2: .......... done [curamd64-setuptools-job-01] `-- Extracting py311-more-itertools-10.6.0: .......... done [curamd64-setuptools-job-01] `-- Installing py311-packaging-26.2... [curamd64-setuptools-job-01] `-- Extracting py311-packaging-26.2: .......... done [curamd64-setuptools-job-01] `-- Installing py311-wheel-0.47.0... [curamd64-setuptools-job-01] `-- Extracting py311-wheel-0.47.0: .......... done [curamd64-setuptools-job-01] Extracting py311-setuptools-81.0.0: .......... done ===== Message from python311-3.11.15_2: -- 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-python-nexus-2.9.0_1 depends on package: py311-setuptools>=63.1.0 - found ===> Returning to build of py311-python-nexus-2.9.0_1 ===> py311-python-nexus-2.9.0_1 depends on file: /usr/local/bin/python3.11 - 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 py311-python-nexus-2.9.0_1 /usr/local/lib/python3.11/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 py311-python-nexus-2.9.0_1 /usr/local/lib/python3.11/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/__init__.py -> build/lib/nexus copying src/nexus/__main__.py -> build/lib/nexus copying src/nexus/checker.py -> build/lib/nexus copying src/nexus/cli_util.py -> build/lib/nexus copying src/nexus/exceptions.py -> build/lib/nexus copying src/nexus/reader.py -> build/lib/nexus copying src/nexus/util.py -> build/lib/nexus copying src/nexus/writer.py -> build/lib/nexus creating build/lib/nexus/commands copying src/nexus/commands/__init__.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/combine.py -> build/lib/nexus/commands copying src/nexus/commands/convert.py -> build/lib/nexus/commands copying src/nexus/commands/deinterleave.py -> build/lib/nexus/commands copying src/nexus/commands/describecharacter.py -> build/lib/nexus/commands copying src/nexus/commands/describetaxa.py -> build/lib/nexus/commands copying src/nexus/commands/edit.py -> build/lib/nexus/commands copying src/nexus/commands/multistate2binary.py -> build/lib/nexus/commands copying src/nexus/commands/randomise.py -> build/lib/nexus/commands copying src/nexus/commands/tally.py -> build/lib/nexus/commands copying src/nexus/commands/trees.py -> build/lib/nexus/commands creating build/lib/nexus/handlers copying src/nexus/handlers/__init__.py -> build/lib/nexus/handlers copying src/nexus/handlers/data.py -> build/lib/nexus/handlers copying src/nexus/handlers/taxa.py -> build/lib/nexus/handlers copying src/nexus/handlers/tree.py -> build/lib/nexus/handlers creating build/lib/nexus/tools copying src/nexus/tools/__init__.py -> build/lib/nexus/tools copying src/nexus/tools/binarise.py -> build/lib/nexus/tools copying src/nexus/tools/check_zeros.py -> build/lib/nexus/tools copying src/nexus/tools/combine_nexuses.py -> build/lib/nexus/tools copying src/nexus/tools/multistatise.py -> build/lib/nexus/tools copying src/nexus/tools/shufflenexus.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 copying src/nexus/tools/util.py -> build/lib/nexus/tools =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-python-nexus-2.9.0_1 depends on package: py311-clldutils>=0 - not found ===> Installing existing package /packages/All/py311-clldutils-3.24.2_2.pkg [curamd64-setuptools-job-01] Installing py311-clldutils-3.24.2_2... [curamd64-setuptools-job-01] `-- Installing py311-attrs-26.1.0... [curamd64-setuptools-job-01] `-- Extracting py311-attrs-26.1.0: .......... done [curamd64-setuptools-job-01] `-- Installing py311-colorlog-6.9.0... [curamd64-setuptools-job-01] `-- Extracting py311-colorlog-6.9.0: .......... done [curamd64-setuptools-job-01] `-- Installing py311-lxml-6.1.0... [curamd64-setuptools-job-01] | `-- Installing libxml2-2.15.3... [curamd64-setuptools-job-01] | `-- Extracting libxml2-2.15.3: .......... done [curamd64-setuptools-job-01] | `-- Installing libxslt-1.1.45... [curamd64-setuptools-job-01] | | `-- Installing libgcrypt-1.12.2... [curamd64-setuptools-job-01] | | `-- Installing libgpg-error-1.60... [curamd64-setuptools-job-01] | | `-- Extracting libgpg-error-1.60: .......... done [curamd64-setuptools-job-01] | | `-- Extracting libgcrypt-1.12.2: .......... done [curamd64-setuptools-job-01] | `-- Extracting libxslt-1.1.45: .......... done [curamd64-setuptools-job-01] `-- Extracting py311-lxml-6.1.0: .......... done [curamd64-setuptools-job-01] `-- Installing py311-markdown-3.10.2... [curamd64-setuptools-job-01] `-- Extracting py311-markdown-3.10.2: .......... done [curamd64-setuptools-job-01] `-- Installing py311-markupsafe-3.0.3... [curamd64-setuptools-job-01] `-- Extracting py311-markupsafe-3.0.3: .......... done [curamd64-setuptools-job-01] `-- Installing py311-python-dateutil-2.9.0... [curamd64-setuptools-job-01] | `-- Installing py311-six-1.17.0... [curamd64-setuptools-job-01] | `-- Extracting py311-six-1.17.0: .......... done [curamd64-setuptools-job-01] `-- Extracting py311-python-dateutil-2.9.0: .......... done [curamd64-setuptools-job-01] `-- Installing py311-tabulate-0.9.0... [curamd64-setuptools-job-01] `-- Extracting py311-tabulate-0.9.0: .......... done [curamd64-setuptools-job-01] Extracting py311-clldutils-3.24.2_2: .......... done ===> py311-python-nexus-2.9.0_1 depends on package: py311-clldutils>=0 - found ===> Returning to build of py311-python-nexus-2.9.0_1 ===> py311-python-nexus-2.9.0_1 depends on package: py311-termcolor>=0 - not found ===> Installing existing package /packages/All/py311-termcolor-3.3.0.pkg [curamd64-setuptools-job-01] Installing py311-termcolor-3.3.0... [curamd64-setuptools-job-01] Extracting py311-termcolor-3.3.0: .......... done ===> py311-python-nexus-2.9.0_1 depends on package: py311-termcolor>=0 - found ===> Returning to build of py311-python-nexus-2.9.0_1 ===> py311-python-nexus-2.9.0_1 depends on package: py311-newick>=0 - not found ===> Installing existing package /packages/All/py311-newick-1.11.0.pkg [curamd64-setuptools-job-01] Installing py311-newick-1.11.0... [curamd64-setuptools-job-01] Extracting py311-newick-1.11.0: .......... done ===> py311-python-nexus-2.9.0_1 depends on package: py311-newick>=0 - found ===> Returning to build of py311-python-nexus-2.9.0_1 ===> py311-python-nexus-2.9.0_1 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Staging for py311-python-nexus-2.9.0_1 ===> Generating temporary packing list /usr/local/lib/python3.11/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/python3.11/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-py311/stage/usr/local/lib/python3.11/site-packages creating /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus copying build/lib/nexus/__init__.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus copying build/lib/nexus/__main__.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus copying build/lib/nexus/checker.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus copying build/lib/nexus/cli_util.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus copying build/lib/nexus/exceptions.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus copying build/lib/nexus/reader.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus copying build/lib/nexus/util.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus copying build/lib/nexus/writer.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus creating /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands copying build/lib/nexus/commands/__init__.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands copying build/lib/nexus/commands/binary2multistate.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands copying build/lib/nexus/commands/check.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands copying build/lib/nexus/commands/combine.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands copying build/lib/nexus/commands/convert.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands copying build/lib/nexus/commands/deinterleave.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands copying build/lib/nexus/commands/describecharacter.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands copying build/lib/nexus/commands/describetaxa.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands copying build/lib/nexus/commands/edit.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands copying build/lib/nexus/commands/multistate2binary.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands copying build/lib/nexus/commands/randomise.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands copying build/lib/nexus/commands/tally.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands copying build/lib/nexus/commands/trees.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands creating /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/handlers copying build/lib/nexus/handlers/__init__.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/handlers copying build/lib/nexus/handlers/data.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/handlers copying build/lib/nexus/handlers/taxa.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/handlers copying build/lib/nexus/handlers/tree.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/handlers creating /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/tools copying build/lib/nexus/tools/__init__.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/tools copying build/lib/nexus/tools/binarise.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/tools copying build/lib/nexus/tools/check_zeros.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/tools copying build/lib/nexus/tools/combine_nexuses.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/tools copying build/lib/nexus/tools/multistatise.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/tools copying build/lib/nexus/tools/shufflenexus.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/tools copying build/lib/nexus/tools/sites.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/tools copying build/lib/nexus/tools/trees.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/tools copying build/lib/nexus/tools/util.py -> /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/tools byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/__main__.py to __main__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/checker.py to checker.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/cli_util.py to cli_util.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/exceptions.py to exceptions.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/reader.py to reader.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/util.py to util.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/writer.py to writer.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands/binary2multistate.py to binary2multistate.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands/check.py to check.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands/combine.py to combine.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands/convert.py to convert.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands/deinterleave.py to deinterleave.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands/describecharacter.py to describecharacter.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands/describetaxa.py to describetaxa.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands/edit.py to edit.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands/multistate2binary.py to multistate2binary.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands/randomise.py to randomise.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands/tally.py to tally.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/commands/trees.py to trees.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/handlers/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/handlers/data.py to data.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/handlers/taxa.py to taxa.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/handlers/tree.py to tree.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/tools/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/tools/binarise.py to binarise.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/tools/check_zeros.py to check_zeros.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/tools/combine_nexuses.py to combine_nexuses.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/tools/multistatise.py to multistatise.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/tools/shufflenexus.py to shufflenexus.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/tools/sites.py to sites.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/tools/trees.py to trees.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/lib/python3.11/site-packages/nexus/tools/util.py to util.cpython-311.pyc writing byte-compilation script '/tmp/tmpdd_ek75f.py' /usr/local/bin/python3.11 /tmp/tmpdd_ek75f.py removing /tmp/tmpdd_ek75f.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-py311/stage/usr/local/lib/python3.11/site-packages/python_nexus-2.9.0-py3.11.egg-info running install_scripts Installing nexus script to /wrkdirs/usr/ports/biology/python-nexus/work-py311/stage/usr/local/bin writing list of installed files to '/wrkdirs/usr/ports/biology/python-nexus/work-py311/.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=2026-06-05T11:43:28+0000' 'PKG_NOTE_ports_top_git_hash=a8b187544' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=a8b187544' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.4' NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building packages for py311-python-nexus-2.9.0_1 ===> Building py311-python-nexus-2.9.0_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py311-python-nexus-2.9.0_1 build of biology/python-nexus@py311 | py311-python-nexus-2.9.0_1 ended at Fri Jun 5 20:46:49 JST 2026 build time: 00:04:52