=>> Building biology/py-biom-format build started at Wed Jul 8 01:16:49 JST 2026 port directory: /usr/ports/biology/py-biom-format package name: py312-biom-format-2.1.16_3 building for: FreeBSD s15amd64-setuptools2-job-01 15.1-STABLE FreeBSD 15.1-STABLE 1501501 amd64 maintained by: jrm@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 956 Jul 5 18:52 /usr/ports/biology/py-biom-format/Makefile Ports top last git commit: 18628b9022c9c1c0e7cb5e71c2aa1e1e563ca34a Ports top unclean checkout: yes Port dir last git commit: 2bf3834a197ccf8956332378eda8dd7577965246 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.8 Host OSVERSION: 1501501 Jail OSVERSION: 1501501 Job Id: 01 ---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-setuptools2/01/.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-- jrm@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.12" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-biom-format/work-py312 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-biom-format/work-py312 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-biom-format/work-py312/.cache HOME=/wrkdirs/usr/ports/biology/py-biom-format/work-py312 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-biom-format/work-py312/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-biom-format/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/py-biom-format/work-py312 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-biom-format/work-py312 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-biom-format/work-py312/.cache HOME=/wrkdirs/usr/ports/biology/py-biom-format/work-py312 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-biom-format/work-py312/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-biom-format/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/py312-biom-format" EXAMPLESDIR="share/examples/py312-biom-format" DATADIR="share/py312-biom-format" WWWDIR="www/py312-biom-format" ETCDIR="etc/py312-biom-format" --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/py312-biom-format DOCSDIR=/usr/local/share/doc/py312-biom-format EXAMPLESDIR=/usr/local/share/examples/py312-biom-format WWWDIR=/usr/local/www/py312-biom-format ETCDIR=/usr/local/etc/py312-biom-format --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 #### #### 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-biom-format-2.1.16_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.7.5.pkg [s15amd64-setuptools2-job-01] Installing pkg-2.7.5... [s15amd64-setuptools2-job-01] Extracting pkg-2.7.5: .......... done ===> py312-biom-format-2.1.16_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py312-biom-format-2.1.16_3 =========================================================================== =================================================== ===== 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 => biom-format-2.1.16.tar.gz doesn't seem to exist in /portdistfiles. => Attempting to fetch https://files.pythonhosted.org/packages/source/b/biom-format/biom-format-2.1.16.tar.gz biom-format-2.1.16.tar.gz 11 MB 37 MBps 01s ===> Fetching all distfiles required by py312-biom-format-2.1.16_3 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py312-biom-format-2.1.16_3 for building => SHA256 Checksum OK for biom-format-2.1.16.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-biom-format-2.1.16_3 for building ===> Extracting for py312-biom-format-2.1.16_3 => SHA256 Checksum OK for biom-format-2.1.16.tar.gz. /bin/rm -f -r /wrkdirs/usr/ports/biology/py-biom-format/work-py312/biom-format-2.1.16/tests =========================================================================== =================================================== ===== 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-biom-format-2.1.16_3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py312-biom-format-2.1.16_3 depends on package: py312-numpy>=1.16 - not found ===> Installing existing package /packages/All/py312-numpy-2.4.6_1,1.pkg [s15amd64-setuptools2-job-01] Installing py312-numpy-2.4.6_1,1... [s15amd64-setuptools2-job-01] `-- Installing gcc14-14.2.0_6... [s15amd64-setuptools2-job-01] | `-- Installing binutils-2.44,1... [s15amd64-setuptools2-job-01] | | `-- Installing indexinfo-0.3.1_1... [s15amd64-setuptools2-job-01] | | `-- Extracting indexinfo-0.3.1_1: .... done [s15amd64-setuptools2-job-01] | | `-- Installing zstd-1.5.7_2... [s15amd64-setuptools2-job-01] | | `-- Installing liblz4-1.10.0_2,1... [s15amd64-setuptools2-job-01] | | `-- Extracting liblz4-1.10.0_2,1: .......... done [s15amd64-setuptools2-job-01] | | `-- Extracting zstd-1.5.7_2: .......... done [s15amd64-setuptools2-job-01] | `-- Extracting binutils-2.44,1: .......... done [s15amd64-setuptools2-job-01] | `-- Installing gmp-6.3.0... [s15amd64-setuptools2-job-01] | `-- Extracting gmp-6.3.0: .......... done [s15amd64-setuptools2-job-01] | `-- Installing mpc-1.4.1... [s15amd64-setuptools2-job-01] | | `-- Installing mpfr-4.2.2,1... [s15amd64-setuptools2-job-01] | | `-- Extracting mpfr-4.2.2,1: .......... done [s15amd64-setuptools2-job-01] | `-- Extracting mpc-1.4.1: .......... done [s15amd64-setuptools2-job-01] `-- Extracting gcc14-14.2.0_6: .......... done [s15amd64-setuptools2-job-01] `-- Installing openblas-0.3.33,2... [s15amd64-setuptools2-job-01] `-- Extracting openblas-0.3.33,2: .......... done [s15amd64-setuptools2-job-01] `-- Installing python312-3.12.13_3... [s15amd64-setuptools2-job-01] | `-- Installing expat-2.8.2... [s15amd64-setuptools2-job-01] | `-- Extracting expat-2.8.2: .......... done [s15amd64-setuptools2-job-01] | `-- Installing gettext-runtime-1.0_1... [s15amd64-setuptools2-job-01] | `-- Extracting gettext-runtime-1.0_1: .......... done [s15amd64-setuptools2-job-01] | `-- Installing libffi-3.6.0... [s15amd64-setuptools2-job-01] | `-- Extracting libffi-3.6.0: .......... done [s15amd64-setuptools2-job-01] | `-- Installing mpdecimal-4.0.1... [s15amd64-setuptools2-job-01] | `-- Extracting mpdecimal-4.0.1: .......... done [s15amd64-setuptools2-job-01] | `-- Installing openssl-3.0.21,1... [s15amd64-setuptools2-job-01] | `-- Extracting openssl-3.0.21,1: .......... done [s15amd64-setuptools2-job-01] | `-- Installing readline-8.3.3... [s15amd64-setuptools2-job-01] | `-- Extracting readline-8.3.3: .......... done [s15amd64-setuptools2-job-01] `-- Extracting python312-3.12.13_3: .......... done [s15amd64-setuptools2-job-01] Extracting py312-numpy-2.4.6_1,1: .......... done ===== Message from gcc14-14.2.0_6: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc14 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===== 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-biom-format-2.1.16_3 depends on package: py312-numpy>=1.16 - found ===> Returning to build of py312-biom-format-2.1.16_3 ===> py312-biom-format-2.1.16_3 depends on package: py312-cython>=3.2.4 - not found ===> Installing existing package /packages/All/py312-cython-3.2.4.pkg [s15amd64-setuptools2-job-01] Installing py312-cython-3.2.4... [s15amd64-setuptools2-job-01] Extracting py312-cython-3.2.4: .......... done ===> py312-biom-format-2.1.16_3 depends on package: py312-cython>=3.2.4 - found ===> Returning to build of py312-biom-format-2.1.16_3 ===> py312-biom-format-2.1.16_3 depends on package: py312-setuptools>=63.1.0 - not found ===> Installing existing package /packages/All/py312-setuptools-81.0.0.pkg [s15amd64-setuptools2-job-01] Installing py312-setuptools-81.0.0... [s15amd64-setuptools2-job-01] `-- Installing py312-more-itertools-11.1.0... [s15amd64-setuptools2-job-01] `-- Extracting py312-more-itertools-11.1.0: .......... done [s15amd64-setuptools2-job-01] `-- Installing py312-packaging-26.2... [s15amd64-setuptools2-job-01] `-- Extracting py312-packaging-26.2: .......... done [s15amd64-setuptools2-job-01] `-- Installing py312-wheel-0.47.0... [s15amd64-setuptools2-job-01] `-- Extracting py312-wheel-0.47.0: .......... done [s15amd64-setuptools2-job-01] Extracting py312-setuptools-81.0.0: .......... done ===> py312-biom-format-2.1.16_3 depends on package: py312-setuptools>=63.1.0 - found ===> Returning to build of py312-biom-format-2.1.16_3 ===> py312-biom-format-2.1.16_3 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-biom-format-2.1.16_3 setup.py:15: SetuptoolsDeprecationWarning: The test command is disabled and references to it are deprecated. !! ******************************************************************************** Please remove any references to `setuptools.command.test` in all supported versions of the affected package. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. ******************************************************************************** !! from setuptools.command.test import test as TestCommand Compiling biom/_filter.pyx because it changed. Compiling biom/_transform.pyx because it changed. Compiling biom/_subsample.pyx because it changed. [1/3] Cythonizing biom/_filter.pyx [2/3] Cythonizing biom/_subsample.pyx [3/3] Cythonizing biom/_transform.pyx /usr/local/lib/python3.12/site-packages/setuptools/_distutils/dist.py:287: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) /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-biom-format-2.1.16_3 setup.py:15: SetuptoolsDeprecationWarning: The test command is disabled and references to it are deprecated. !! ******************************************************************************** Please remove any references to `setuptools.command.test` in all supported versions of the affected package. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. ******************************************************************************** !! from setuptools.command.test import test as TestCommand /usr/local/lib/python3.12/site-packages/setuptools/_distutils/dist.py:287: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) /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.freebsd-15.1-STABLE-amd64-cpython-312/biom copying biom/exception.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom copying biom/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom copying biom/table.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom copying biom/util.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom copying biom/parse.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom copying biom/err.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests copying biom/tests/test_util.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests copying biom/tests/test_err.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests copying biom/tests/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests copying biom/tests/test_table.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests copying biom/tests/long_lines.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests copying biom/tests/test_parse.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli copying biom/cli/metadata_adder.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli copying biom/cli/table_normalizer.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli copying biom/cli/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli copying biom/cli/table_converter.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli copying biom/cli/installation_informer.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli copying biom/cli/table_summarizer.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli copying biom/cli/util.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli copying biom/cli/table_subsetter.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli copying biom/cli/metadata_exporter.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli copying biom/cli/uc_processor.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli copying biom/cli/table_validator.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli copying biom/cli/table_head.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli copying biom/cli/table_ids.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli copying biom/tests/test_cli/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli copying biom/tests/test_cli/test_show_install_info.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli copying biom/tests/test_cli/test_subset_table.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli copying biom/tests/test_cli/test_validate_table.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli copying biom/tests/test_cli/test_uc_processor.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli copying biom/tests/test_cli/test_table_normalizer.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli copying biom/tests/test_cli/test_table_converter.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli copying biom/tests/test_cli/test_add_metadata.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli copying biom/tests/test_cli/test_summarize_table.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_data copying biom/tests/test_data/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_data running egg_info writing biom_format.egg-info/PKG-INFO writing dependency_links to biom_format.egg-info/dependency_links.txt writing entry points to biom_format.egg-info/entry_points.txt writing requirements to biom_format.egg-info/requires.txt writing top-level names to biom_format.egg-info/top_level.txt dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative reading manifest file 'biom_format.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no directories found matching 'support_files' warning: no directories found matching 'tests/test_data' no previously-included directories found matching 'docs/_build' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '.git' found anywhere in distribution warning: no previously-included files matching '*.so' found anywhere in distribution warning: no previously-included files matching '.*.swp' found anywhere in distribution adding license file 'COPYING.txt' writing manifest file 'biom_format.egg-info/SOURCES.txt' /usr/local/lib/python3.12/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'biom.assets' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'biom.assets' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'biom.assets' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'biom.assets' to be distributed and are already explicitly excluding 'biom.assets' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/local/lib/python3.12/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'biom.tests.bench_tables' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'biom.tests.bench_tables' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'biom.tests.bench_tables' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'biom.tests.bench_tables' to be distributed and are already explicitly excluding 'biom.tests.bench_tables' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/local/lib/python3.12/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'biom.tests.test_cli.test_data' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'biom.tests.test_cli.test_data' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'biom.tests.test_cli.test_data' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'biom.tests.test_cli.test_data' to be distributed and are already explicitly excluding 'biom.tests.test_cli.test_data' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying biom/_filter.pyx -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom copying biom/_subsample.pyx -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom copying biom/_transform.pyx -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/assets copying biom/assets/exercise_api.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/assets copying biom/assets/exercise_cli.sh -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/assets creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.001_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.010_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.100_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.001_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.010_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.100_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.001_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.010_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.100_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.001_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.010_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.100_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.001_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.010_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.100_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.001_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.010_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.100_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.001_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.010_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.100_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.001_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.010_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.100_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.001_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.010_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.100_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.001_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.010_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.100_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.001_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.010_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.100_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.001_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.010_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.100_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.001_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.010_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.100_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.001_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.010_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.100_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.001_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.010_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.100_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.001_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.010_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.100_bench.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/json_obs_collapsed.biom -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/json_sample_collapsed.biom -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/test.biom -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/test.json -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli/test_data copying biom/tests/test_data/bad_table.txt -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_data copying biom/tests/test_data/bad_table.txt.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_data copying biom/tests/test_data/edgecase_issue_952.biom -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_data copying biom/tests/test_data/empty.biom -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_data copying biom/tests/test_data/no-contents.biom -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_data copying biom/tests/test_data/test.biom -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_data copying biom/tests/test_data/test.json -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_data copying biom/tests/test_data/test.json.gz -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_data copying biom/tests/test_data/test_grp_metadata.biom -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_data running build_ext building 'biom._filter' extension creating build/temp.freebsd-15.1-STABLE-amd64-cpython-312/biom cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.12/site-packages/numpy/_core/include -I/usr/local/lib/python3.12/site-packages/numpy/_core/include -I/usr/local/include/python3.12 -c biom/_filter.c -o build/temp.freebsd-15.1-STABLE-amd64-cpython-312/biom/_filter.o cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-15.1-STABLE-amd64-cpython-312/biom/_filter.o -L/usr/local/lib -o build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/_filter.cpython-312.so building 'biom._transform' extension cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.12/site-packages/numpy/_core/include -I/usr/local/lib/python3.12/site-packages/numpy/_core/include -I/usr/local/include/python3.12 -c biom/_transform.c -o build/temp.freebsd-15.1-STABLE-amd64-cpython-312/biom/_transform.o cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-15.1-STABLE-amd64-cpython-312/biom/_transform.o -L/usr/local/lib -o build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/_transform.cpython-312.so building 'biom._subsample' extension cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.12/site-packages/numpy/_core/include -I/usr/local/lib/python3.12/site-packages/numpy/_core/include -I/usr/local/include/python3.12 -c biom/_subsample.c -o build/temp.freebsd-15.1-STABLE-amd64-cpython-312/biom/_subsample.o cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-15.1-STABLE-amd64-cpython-312/biom/_subsample.o -L/usr/local/lib -o build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/_subsample.cpython-312.so =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py312-biom-format-2.1.16_3 depends on package: py312-click>0 - not found ===> Installing existing package /packages/All/py312-click-8.3.1.pkg [s15amd64-setuptools2-job-01] Installing py312-click-8.3.1... [s15amd64-setuptools2-job-01] Extracting py312-click-8.3.1: .......... done ===> py312-biom-format-2.1.16_3 depends on package: py312-click>0 - found ===> Returning to build of py312-biom-format-2.1.16_3 ===> py312-biom-format-2.1.16_3 depends on package: py312-numpy>=1.16 - found ===> py312-biom-format-2.1.16_3 depends on package: py312-scipy>=1.3.1 - not found ===> Installing existing package /packages/All/py312-scipy-1.17.1_3,1.pkg [s15amd64-setuptools2-job-01] Installing py312-scipy-1.17.1_3,1... [s15amd64-setuptools2-job-01] `-- Installing qhull-8.0.2_3,1... [s15amd64-setuptools2-job-01] `-- Extracting qhull-8.0.2_3,1: .......... done [s15amd64-setuptools2-job-01] Extracting py312-scipy-1.17.1_3,1: .......... done ===> py312-biom-format-2.1.16_3 depends on package: py312-scipy>=1.3.1 - found ===> Returning to build of py312-biom-format-2.1.16_3 ===> py312-biom-format-2.1.16_3 depends on package: py312-pandas>=0.20.0 - not found ===> Installing existing package /packages/All/py312-pandas-2.3.3_3,1.pkg [s15amd64-setuptools2-job-01] Installing py312-pandas-2.3.3_3,1... [s15amd64-setuptools2-job-01] `-- Installing py312-bottleneck-1.6.0_2... [s15amd64-setuptools2-job-01] `-- Extracting py312-bottleneck-1.6.0_2: .......... done [s15amd64-setuptools2-job-01] `-- Installing py312-numexpr-2.14.1_2... [s15amd64-setuptools2-job-01] `-- Extracting py312-numexpr-2.14.1_2: .......... done [s15amd64-setuptools2-job-01] `-- Installing py312-python-dateutil-2.9.0... [s15amd64-setuptools2-job-01] | `-- Installing py312-six-1.17.0... [s15amd64-setuptools2-job-01] | `-- Extracting py312-six-1.17.0: .......... done [s15amd64-setuptools2-job-01] `-- Extracting py312-python-dateutil-2.9.0: .......... done [s15amd64-setuptools2-job-01] `-- Installing py312-pytz-2026.2,1... [s15amd64-setuptools2-job-01] `-- Extracting py312-pytz-2026.2,1: .......... done [s15amd64-setuptools2-job-01] `-- Installing py312-sqlite3-3.12.13_10... [s15amd64-setuptools2-job-01] | `-- Installing sqlite3-3.53.3,1... [s15amd64-setuptools2-job-01] | | `-- Installing libedit-3.1.20260512,1... [s15amd64-setuptools2-job-01] | | `-- Extracting libedit-3.1.20260512,1: .......... done [s15amd64-setuptools2-job-01] | `-- Extracting sqlite3-3.53.3,1: .......... done [s15amd64-setuptools2-job-01] `-- Extracting py312-sqlite3-3.12.13_10: ......... done [s15amd64-setuptools2-job-01] `-- Installing py312-tzdata-2026.2... [s15amd64-setuptools2-job-01] `-- Extracting py312-tzdata-2026.2: .......... done [s15amd64-setuptools2-job-01] Extracting py312-pandas-2.3.3_3,1: .......... done ===== Message from py312-pandas-2.3.3_3,1: -- Install math/py-statsmodels to enable parts of pandas.stats. Install devel/py-xarray to enable the to_xarray() function. ===> py312-biom-format-2.1.16_3 depends on package: py312-pandas>=0.20.0 - found ===> Returning to build of py312-biom-format-2.1.16_3 ===> py312-biom-format-2.1.16_3 depends on package: py312-h5py>=2.2.0 - not found ===> Installing existing package /packages/All/py312-h5py-3.16.0_1.pkg [s15amd64-setuptools2-job-01] Installing py312-h5py-3.16.0_1... [s15amd64-setuptools2-job-01] `-- Installing hdf5-1.12.2_2,1... [s15amd64-setuptools2-job-01] | `-- Installing libaec-1.1.7... [s15amd64-setuptools2-job-01] | `-- Extracting libaec-1.1.7: .......... done [s15amd64-setuptools2-job-01] `-- Extracting hdf5-1.12.2_2,1: .......... done [s15amd64-setuptools2-job-01] Extracting py312-h5py-3.16.0_1: .......... done ===> py312-biom-format-2.1.16_3 depends on package: py312-h5py>=2.2.0 - found ===> Returning to build of py312-biom-format-2.1.16_3 ===> py312-biom-format-2.1.16_3 depends on file: /usr/local/bin/python3.12 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Staging for py312-biom-format-2.1.16_3 ===> Generating temporary packing list setup.py:15: SetuptoolsDeprecationWarning: The test command is disabled and references to it are deprecated. !! ******************************************************************************** Please remove any references to `setuptools.command.test` in all supported versions of the affected package. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. ******************************************************************************** !! from setuptools.command.test import test as TestCommand /usr/local/lib/python3.12/site-packages/setuptools/_distutils/dist.py:287: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) /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 egg_info writing biom_format.egg-info/PKG-INFO writing dependency_links to biom_format.egg-info/dependency_links.txt writing entry points to biom_format.egg-info/entry_points.txt writing requirements to biom_format.egg-info/requires.txt writing top-level names to biom_format.egg-info/top_level.txt dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative reading manifest file 'biom_format.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no directories found matching 'support_files' warning: no directories found matching 'tests/test_data' no previously-included directories found matching 'docs/_build' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '.git' found anywhere in distribution warning: no previously-included files matching '*.so' found anywhere in distribution warning: no previously-included files matching '.*.swp' found anywhere in distribution adding license file 'COPYING.txt' writing manifest file 'biom_format.egg-info/SOURCES.txt' /usr/local/lib/python3.12/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'biom.assets' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'biom.assets' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'biom.assets' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'biom.assets' to be distributed and are already explicitly excluding 'biom.assets' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/local/lib/python3.12/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'biom.tests.bench_tables' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'biom.tests.bench_tables' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'biom.tests.bench_tables' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'biom.tests.bench_tables' to be distributed and are already explicitly excluding 'biom.tests.bench_tables' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/local/lib/python3.12/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'biom.tests.test_cli.test_data' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'biom.tests.test_cli.test_data' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'biom.tests.test_cli.test_data' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'biom.tests.test_cli.test_data' to be distributed and are already explicitly excluding 'biom.tests.test_cli.test_data' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) running build_ext running install_lib creating /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages creating /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/exception.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/_subsample.pyx -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom creating /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_util.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_err.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/__init__.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests creating /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli/__init__.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli/test_show_install_info.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli/test_subset_table.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli/test_validate_table.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli/test_uc_processor.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli creating /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli/test_data copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli/test_data/test.biom -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli/test_data copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli/test_data/json_sample_collapsed.biom -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli/test_data copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli/test_data/test.json -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli/test_data copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli/test_data/json_obs_collapsed.biom -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli/test_data copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli/test_table_normalizer.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli/test_table_converter.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli/test_add_metadata.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_cli/test_summarize_table.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_table.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/long_lines.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests creating /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_data copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_data/bad_table.txt -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_data copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_data/no-contents.biom -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_data copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_data/bad_table.txt.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_data copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_data/edgecase_issue_952.biom -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_data copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_data/__init__.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_data copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_data/empty.biom -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_data copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_data/test.biom -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_data copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_data/test.json.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_data copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_data/test.json -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_data copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_data/test_grp_metadata.biom -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_data creating /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x10000x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x1000x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x100x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x100x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x10x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x1000x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x1000x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x1000x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x10x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x10000x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x10x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x10x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x100x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x1000x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x10000x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x10000x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x1000x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x100x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x1000x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x100x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x1000x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x1000x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x10000x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x1000x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x1000x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x100x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x1000x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x100x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x10000x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x10000x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x10000x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x100x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x10000x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x1000x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x10x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x10x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x1000x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x1000x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x10000x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x100x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x10000x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x10x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x100x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x100x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x10x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x10x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x100x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x10x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x10000x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x10000x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x10x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x10x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x10x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x1000x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x10x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x1000x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x10x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x100x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x10000x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x1000x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x10000x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x1000x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x100x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x100x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x10000x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x10000x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x10000x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x1000x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x100x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x100x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x1000x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x10x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x100x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x10000x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x10x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x10x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x10x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x1000x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x10000x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x100x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x10000x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x100x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x10x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x10000x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/100x10x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x1000x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x1000x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x10000x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x10x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x100x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x100x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x10x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10000x100x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x10x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/10x100x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/bench_tables/1000x10000x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/bench_tables copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/tests/test_parse.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/__init__.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/table.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/_subsample.cpython-312.so -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/_transform.cpython-312.so -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/util.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/_filter.pyx -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/parse.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/_transform.pyx -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom creating /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli/metadata_adder.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli/table_normalizer.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli/__init__.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli/table_converter.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli/installation_informer.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli/table_summarizer.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli/util.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli/table_subsetter.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli/metadata_exporter.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli/uc_processor.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli/table_validator.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli/table_head.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/cli/table_ids.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/err.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom creating /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/assets copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/assets/exercise_cli.sh -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/assets copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/assets/exercise_api.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/assets copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/biom/_filter.cpython-312.so -> /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/exception.py to exception.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_util.py to test_util.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_err.py to test_err.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/__init__.py to __init__.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli/__init__.py to __init__.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli/test_show_install_info.py to test_show_install_info.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli/test_subset_table.py to test_subset_table.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli/test_validate_table.py to test_validate_table.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli/test_uc_processor.py to test_uc_processor.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli/test_table_normalizer.py to test_table_normalizer.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli/test_table_converter.py to test_table_converter.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli/test_add_metadata.py to test_add_metadata.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_cli/test_summarize_table.py to test_summarize_table.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_table.py to test_table.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/long_lines.py to long_lines.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_data/__init__.py to __init__.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/tests/test_parse.py to test_parse.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/__init__.py to __init__.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/table.py to table.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/util.py to util.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/parse.py to parse.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli/metadata_adder.py to metadata_adder.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli/table_normalizer.py to table_normalizer.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli/__init__.py to __init__.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli/table_converter.py to table_converter.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli/installation_informer.py to installation_informer.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli/table_summarizer.py to table_summarizer.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli/util.py to util.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli/table_subsetter.py to table_subsetter.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli/metadata_exporter.py to metadata_exporter.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli/uc_processor.py to uc_processor.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli/table_validator.py to table_validator.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli/table_head.py to table_head.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/cli/table_ids.py to table_ids.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/err.py to err.cpython-312.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/assets/exercise_api.py to exercise_api.cpython-312.pyc writing byte-compilation script '/tmp/tmpy0dtan6o.py' /usr/local/bin/python3.12 /tmp/tmpy0dtan6o.py removing /tmp/tmpy0dtan6o.py running install_egg_info Copying biom_format.egg-info to /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom_format-2.1.16-py3.12.egg-info running install_scripts Installing biom script to /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/bin writing list of installed files to '/wrkdirs/usr/ports/biology/py-biom-format/work-py312/.PLIST.pymodtmp' /usr/bin/strip /wrkdirs/usr/ports/biology/py-biom-format/work-py312/stage/usr/local/lib/python3.12/site-packages/biom/*.so ===> Creating unique files: Move MAN files needing SUFFIX ===> Creating unique files: Move files needing SUFFIX Move: bin/biom --> bin/biom-3.12 Link: @bin/biom --> bin/biom-3.12 ====> 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=2026-07-07T16:16:49+0000' 'PKG_NOTE_ports_top_git_hash=18628b9022c9c1c0e7cb5e71c2aa1e1e563ca34a' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=2bf3834a197ccf8956332378eda8dd7577965246' '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-biom-format-2.1.16_3 ===> Building py312-biom-format-2.1.16_3 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py312-biom-format-2.1.16_3 build of biology/py-biom-format@py312 | py312-biom-format-2.1.16_3 ended at Wed Jul 8 01:19:51 JST 2026 build time: 00:03:56