=>> Building biology/py-biom-format build started at Sun Dec 14 23:16:42 EST 2025 port directory: /usr/ports/biology/py-biom-format package name: py311-biom-format-2.1.16_1 building for: FreeBSD pkg.DaveG.ca 14.3-RELEASE-p1 FreeBSD 14.3-RELEASE-p1 1403000 amd64 maintained by: jrm@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 854 Mar 10 2025 /usr/ports/biology/py-biom-format/Makefile Ports top last git commit: 10f7dee57a4c Ports top unclean checkout: no Port dir last git commit: 06a08e69f3ac Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1403000 Job Id: 16 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1403000 UNAME_v=FreeBSD 14.3-RELEASE-p1 1403000 UNAME_r=14.3-RELEASE-p1 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_14_3_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_14_3_x64-HEAD-ALL/16/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_3_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_3_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py311 MAKE_ARGS= FLAVOR=py311 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jrm@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-biom-format/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-biom-format/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-biom-format/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-biom-format/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-biom-format/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-biom-format/work-py311/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-biom-format/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-biom-format/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-biom-format/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-biom-format/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-biom-format/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-biom-format/work-py311/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=14.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/py311-biom-format" EXAMPLESDIR="share/examples/py311-biom-format" DATADIR="share/py311-biom-format" WWWDIR="www/py311-biom-format" ETCDIR="etc/py311-biom-format" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/py311-biom-format DOCSDIR=/usr/local/share/doc/py311-biom-format EXAMPLESDIR=/usr/local/share/examples/py311-biom-format WWWDIR=/usr/local/www/py311-biom-format ETCDIR=/usr/local/etc/py311-biom-format --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-biom-format-2.1.16_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.4.2_1.pkg [pkg.DaveG.ca] Installing pkg-2.4.2_1... [pkg.DaveG.ca] Extracting pkg-2.4.2_1: .......... done ===> py311-biom-format-2.1.16_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py311-biom-format-2.1.16_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py311-biom-format-2.1.16_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py311-biom-format-2.1.16_1 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=root UID=0 GID=0 ===> Fetching all distfiles required by py311-biom-format-2.1.16_1 for building ===> Extracting for py311-biom-format-2.1.16_1 => SHA256 Checksum OK for biom-format-2.1.16.tar.gz. /bin/rm -f -r /wrkdirs/usr/ports/biology/py-biom-format/work-py311/biom-format-2.1.16/tests =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for py311-biom-format-2.1.16_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-biom-format-2.1.16_1 depends on package: py311-numpy>=1.16,1<1.27,1 - not found ===> Installing existing package /packages/All/py311-numpy-1.26.4_11,1.pkg [pkg.DaveG.ca] Installing py311-numpy-1.26.4_11,1... [pkg.DaveG.ca] `-- Installing gcc13-13.3.0_3... [pkg.DaveG.ca] | `-- Installing binutils-2.44,1... [pkg.DaveG.ca] | | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | | `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] | | `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] | `-- Extracting binutils-2.44,1: .......... done [pkg.DaveG.ca] | `-- Installing gmp-6.3.0... [pkg.DaveG.ca] | `-- Extracting gmp-6.3.0: .......... done [pkg.DaveG.ca] | `-- Installing mpc-1.3.1_1... [pkg.DaveG.ca] | | `-- Installing mpfr-4.2.2,1... [pkg.DaveG.ca] | | `-- Extracting mpfr-4.2.2,1: .......... done [pkg.DaveG.ca] | `-- Extracting mpc-1.3.1_1: ...... done [pkg.DaveG.ca] `-- Extracting gcc13-13.3.0_3: .......... done [pkg.DaveG.ca] `-- Installing openblas-0.3.30,2... [pkg.DaveG.ca] `-- Extracting openblas-0.3.30,2: .......... done [pkg.DaveG.ca] `-- Installing python311-3.11.14... [pkg.DaveG.ca] | `-- Installing gettext-runtime-0.23.1... [pkg.DaveG.ca] | `-- Extracting gettext-runtime-0.23.1: .......... done [pkg.DaveG.ca] | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | `-- Installing readline-8.3.1... [pkg.DaveG.ca] | `-- Extracting readline-8.3.1: .......... done [pkg.DaveG.ca] `-- Extracting python311-3.11.14: .......... done [pkg.DaveG.ca] `-- Installing suitesparse-umfpack-6.3.7... [pkg.DaveG.ca] | `-- Installing suitesparse-amd-3.3.4... [pkg.DaveG.ca] | | `-- Installing suitesparse-config-7.12.1... [pkg.DaveG.ca] | | `-- Extracting suitesparse-config-7.12.1: .......... done [pkg.DaveG.ca] | `-- Extracting suitesparse-amd-3.3.4: .......... done [pkg.DaveG.ca] | `-- Installing suitesparse-camd-3.3.5... [pkg.DaveG.ca] | `-- Extracting suitesparse-camd-3.3.5: .......... done [pkg.DaveG.ca] | `-- Installing suitesparse-ccolamd-3.3.5... [pkg.DaveG.ca] | `-- Extracting suitesparse-ccolamd-3.3.5: .......... done [pkg.DaveG.ca] | `-- Installing suitesparse-cholmod-5.3.4... [pkg.DaveG.ca] | | `-- Installing suitesparse-colamd-3.3.5... [pkg.DaveG.ca] | | `-- Extracting suitesparse-colamd-3.3.5: .......... done [pkg.DaveG.ca] | `-- Extracting suitesparse-cholmod-5.3.4: .......... done [pkg.DaveG.ca] `-- Extracting suitesparse-umfpack-6.3.7: .......... done [pkg.DaveG.ca] Extracting py311-numpy-1.26.4_11,1: .......... done ===== Message from gcc13-13.3.0_3: -- 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/gcc13 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===== Message from python311-3.11.14: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> py311-biom-format-2.1.16_1 depends on package: py311-numpy>=1.16,1<1.27,1 - found ===> Returning to build of py311-biom-format-2.1.16_1 ===> py311-biom-format-2.1.16_1 depends on package: py311-cython>=0.29.37<3 - not found ===> Installing existing package /packages/All/py311-cython-0.29.37_2.pkg [pkg.DaveG.ca] Installing py311-cython-0.29.37_2... [pkg.DaveG.ca] Extracting py311-cython-0.29.37_2: .......... done ===> py311-biom-format-2.1.16_1 depends on package: py311-cython>=0.29.37<3 - found ===> Returning to build of py311-biom-format-2.1.16_1 ===> py311-biom-format-2.1.16_1 depends on package: py311-setuptools>=63.1.0 - not found ===> Installing existing package /packages/All/py311-setuptools-63.1.0_3.pkg [pkg.DaveG.ca] Installing py311-setuptools-63.1.0_3... [pkg.DaveG.ca] Extracting py311-setuptools-63.1.0_3: .......... done ===> py311-biom-format-2.1.16_1 depends on package: py311-setuptools>=63.1.0 - found ===> Returning to build of py311-biom-format-2.1.16_1 ===> py311-biom-format-2.1.16_1 depends on file: /usr/local/bin/python3.11 - found ===> py311-biom-format-2.1.16_1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for gcc13 create symlink for gcc13 (world) create symlink for g++13 create symlink for g++13 (world) create symlink for cpp13 create symlink for cpp13 (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> py311-biom-format-2.1.16_1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of py311-biom-format-2.1.16_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for py311-biom-format-2.1.16_1 /usr/local/lib/python3.11/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /wrkdirs/usr/ports/biology/py-biom-format/work-py311/biom-format-2.1.16/biom/_filter.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/local/lib/python3.11/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /wrkdirs/usr/ports/biology/py-biom-format/work-py311/biom-format-2.1.16/biom/_subsample.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/local/lib/python3.11/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /wrkdirs/usr/ports/biology/py-biom-format/work-py311/biom-format-2.1.16/biom/_transform.pyx tree = Parsing.p_module(s, pxd, full_module_name) 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 running config =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for py311-biom-format-2.1.16_1 running build running build_py creating build creating build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311 creating build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom copying biom/exception.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom copying biom/__init__.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom copying biom/table.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom copying biom/util.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom copying biom/parse.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom copying biom/err.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom creating build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests copying biom/tests/test_util.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests copying biom/tests/test_err.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests copying biom/tests/__init__.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests copying biom/tests/test_table.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests copying biom/tests/long_lines.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests copying biom/tests/test_parse.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests creating build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli copying biom/cli/metadata_adder.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli copying biom/cli/table_normalizer.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli copying biom/cli/__init__.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli copying biom/cli/table_converter.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli copying biom/cli/installation_informer.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli copying biom/cli/table_summarizer.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli copying biom/cli/util.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli copying biom/cli/table_subsetter.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli copying biom/cli/metadata_exporter.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli copying biom/cli/uc_processor.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli copying biom/cli/table_validator.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli copying biom/cli/table_head.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli copying biom/cli/table_ids.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli creating build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli copying biom/tests/test_cli/__init__.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli copying biom/tests/test_cli/test_show_install_info.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli copying biom/tests/test_cli/test_subset_table.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli copying biom/tests/test_cli/test_validate_table.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli copying biom/tests/test_cli/test_uc_processor.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli copying biom/tests/test_cli/test_table_normalizer.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli copying biom/tests/test_cli/test_table_converter.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli copying biom/tests/test_cli/test_add_metadata.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli copying biom/tests/test_cli/test_summarize_table.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli creating build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_data copying biom/tests/test_data/__init__.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/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 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/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'biom.assets' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'biom.assets' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'biom.assets' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'biom.assets' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'biom.tests.bench_tables' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'biom.tests.bench_tables' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'biom.tests.bench_tables' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'biom.tests.bench_tables' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'biom.tests.test_cli.test_data' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'biom.tests.test_cli.test_data' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'biom.tests.test_cli.test_data' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'biom.tests.test_cli.test_data' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) copying biom/_filter.pyx -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom copying biom/_subsample.pyx -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom copying biom/_transform.pyx -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom creating build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/assets copying biom/assets/exercise_api.py -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/assets copying biom/assets/exercise_cli.sh -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/assets creating build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.001_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.010_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.100_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.001_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.010_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.100_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.001_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.010_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.100_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.001_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.010_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.100_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.001_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.010_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.100_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.001_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.010_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.100_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.001_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.010_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.100_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.001_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.010_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.100_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.001_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.010_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.100_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.001_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.010_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.100_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.001_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.010_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.100_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.001_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.010_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.100_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.001_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.010_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.100_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.001_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.010_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.100_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.001_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.010_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.100_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.001_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.010_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.100_bench.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables creating build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/json_obs_collapsed.biom -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/json_sample_collapsed.biom -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/test.biom -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/test.json -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli/test_data copying biom/tests/test_data/bad_table.txt -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_data copying biom/tests/test_data/bad_table.txt.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_data copying biom/tests/test_data/edgecase_issue_952.biom -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_data copying biom/tests/test_data/empty.biom -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_data copying biom/tests/test_data/no-contents.biom -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_data copying biom/tests/test_data/test.biom -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_data copying biom/tests/test_data/test.json -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_data copying biom/tests/test_data/test.json.gz -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_data copying biom/tests/test_data/test_grp_metadata.biom -> build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_data running build_ext building 'biom._filter' extension creating build/temp.freebsd-14.3-RELEASE-p1-amd64-cpython-311 creating build/temp.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/usr/local/include/python3.11 -c biom/_filter.c -o build/temp.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/_filter.o In file included from biom/_filter.c:774: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^ 1 warning generated. cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/_filter.o -L/usr/local/lib -o build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/_filter.cpython-311.so building 'biom._transform' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/usr/local/include/python3.11 -c biom/_transform.c -o build/temp.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/_transform.o In file included from biom/_transform.c:774: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^ 1 warning generated. cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/_transform.o -L/usr/local/lib -o build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/_transform.cpython-311.so building 'biom._subsample' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/usr/local/include/python3.11 -c biom/_subsample.c -o build/temp.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/_subsample.o In file included from biom/_subsample.c:774: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^ 1 warning generated. cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/_subsample.o -L/usr/local/lib -o build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/_subsample.cpython-311.so =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-biom-format-2.1.16_1 depends on package: py311-click>0 - not found ===> Installing existing package /packages/All/py311-click-8.1.7_1.pkg [pkg.DaveG.ca] Installing py311-click-8.1.7_1... [pkg.DaveG.ca] Extracting py311-click-8.1.7_1: .......... done ===> py311-biom-format-2.1.16_1 depends on package: py311-click>0 - found ===> Returning to build of py311-biom-format-2.1.16_1 ===> py311-biom-format-2.1.16_1 depends on package: py311-numpy>=1.16,1<1.27,1 - found ===> py311-biom-format-2.1.16_1 depends on package: py311-scipy>=1.3.1 - not found ===> Installing existing package /packages/All/py311-scipy-1.11.1_4,1.pkg [pkg.DaveG.ca] Installing py311-scipy-1.11.1_4,1... [pkg.DaveG.ca] `-- Installing blas-3.12.1... [pkg.DaveG.ca] `-- Extracting blas-3.12.1: ..... done [pkg.DaveG.ca] Extracting py311-scipy-1.11.1_4,1: .......... done ===> py311-biom-format-2.1.16_1 depends on package: py311-scipy>=1.3.1 - found ===> Returning to build of py311-biom-format-2.1.16_1 ===> py311-biom-format-2.1.16_1 depends on package: py311-pandas>=0.20.0 - not found ===> Installing existing package /packages/All/py311-pandas-2.3.3,1.pkg [pkg.DaveG.ca] Installing py311-pandas-2.3.3,1... [pkg.DaveG.ca] `-- Installing py311-bottleneck-1.3.8_1... [pkg.DaveG.ca] `-- Extracting py311-bottleneck-1.3.8_1: .......... done [pkg.DaveG.ca] `-- Installing py311-numexpr-2.14.1... [pkg.DaveG.ca] `-- Extracting py311-numexpr-2.14.1: .......... done [pkg.DaveG.ca] `-- Installing py311-python-dateutil-2.9.0... [pkg.DaveG.ca] | `-- Installing py311-six-1.17.0... [pkg.DaveG.ca] | `-- Extracting py311-six-1.17.0: ........ done [pkg.DaveG.ca] `-- Extracting py311-python-dateutil-2.9.0: .......... done [pkg.DaveG.ca] `-- Installing py311-pytz-2025.2_1,1... [pkg.DaveG.ca] `-- Extracting py311-pytz-2025.2_1,1: .......... done [pkg.DaveG.ca] `-- Installing py311-sqlite3-3.11.14_10... [pkg.DaveG.ca] | `-- Installing sqlite3-3.50.4_2,1... [pkg.DaveG.ca] | | `-- Installing libedit-3.1.20251016_1,1... [pkg.DaveG.ca] | | `-- Extracting libedit-3.1.20251016_1,1: .......... done [pkg.DaveG.ca] | `-- Extracting sqlite3-3.50.4_2,1: .......... done [pkg.DaveG.ca] `-- Extracting py311-sqlite3-3.11.14_10: ...... done [pkg.DaveG.ca] `-- Installing py311-tzdata-2025.2... [pkg.DaveG.ca] `-- Extracting py311-tzdata-2025.2: .......... done [pkg.DaveG.ca] Extracting py311-pandas-2.3.3,1: .......... done ===== Message from py311-pandas-2.3.3,1: -- Install math/py-statsmodels to enable parts of pandas.stats. Install devel/py-xarray to enable the to_xarray() function. ===> py311-biom-format-2.1.16_1 depends on package: py311-pandas>=0.20.0 - found ===> Returning to build of py311-biom-format-2.1.16_1 ===> py311-biom-format-2.1.16_1 depends on package: py311-h5py>=2.2.0 - not found ===> Installing existing package /packages/All/py311-h5py-3.15.1.pkg [pkg.DaveG.ca] Installing py311-h5py-3.15.1... [pkg.DaveG.ca] `-- Installing hdf5-1.12.2_2,1... [pkg.DaveG.ca] | `-- Installing libaec-1.1.4... [pkg.DaveG.ca] | `-- Extracting libaec-1.1.4: .......... done [pkg.DaveG.ca] `-- Extracting hdf5-1.12.2_2,1: .......... done [pkg.DaveG.ca] Extracting py311-h5py-3.15.1: .......... done ===> py311-biom-format-2.1.16_1 depends on package: py311-h5py>=2.2.0 - found ===> Returning to build of py311-biom-format-2.1.16_1 ===> py311-biom-format-2.1.16_1 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for py311-biom-format-2.1.16_1 ===> Generating temporary packing list running install /usr/local/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py 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 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/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'biom.assets' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'biom.assets' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'biom.assets' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'biom.assets' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'biom.tests.bench_tables' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'biom.tests.bench_tables' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'biom.tests.bench_tables' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'biom.tests.bench_tables' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'biom.tests.test_cli.test_data' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'biom.tests.test_cli.test_data' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'biom.tests.test_cli.test_data' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'biom.tests.test_cli.test_data' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) running build_ext running install_lib creating /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11 creating /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages creating /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/exception.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/_subsample.pyx -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom creating /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_util.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_err.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/__init__.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests creating /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli/__init__.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli/test_show_install_info.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli/test_subset_table.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli/test_validate_table.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli/test_uc_processor.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli creating /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli/test_data copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli/test_data/test.biom -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli/test_data copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli/test_data/json_sample_collapsed.biom -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli/test_data copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli/test_data/test.json -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli/test_data copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli/test_data/json_obs_collapsed.biom -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli/test_data copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli/test_table_normalizer.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli/test_table_converter.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli/test_add_metadata.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_cli/test_summarize_table.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_table.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/long_lines.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests creating /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_data copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_data/bad_table.txt -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_data copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_data/no-contents.biom -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_data copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_data/bad_table.txt.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_data copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_data/edgecase_issue_952.biom -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_data copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_data/__init__.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_data copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_data/empty.biom -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_data copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_data/test.biom -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_data copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_data/test.json.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_data copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_data/test.json -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_data copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_data/test_grp_metadata.biom -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_data creating /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x10000x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x1000x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x100x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x100x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x10x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x1000x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x1000x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x1000x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x10x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x10000x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x10x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x10x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x100x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x1000x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x10000x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x10000x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x1000x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x100x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x1000x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x100x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x1000x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x1000x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x10000x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x1000x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x1000x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x100x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x1000x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x100x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x10000x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x10000x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x10000x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x100x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x10000x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x1000x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x10x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x10x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x1000x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x1000x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x10000x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x100x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x10000x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x10x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x100x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x100x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x10x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x10x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x100x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x10x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x10000x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x10000x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x10x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x10x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x10x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x1000x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x10x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x1000x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x10x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x100x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x10000x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x1000x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x10000x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x1000x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x100x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x100x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x10000x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x10000x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x10000x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x1000x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x100x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x100x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x1000x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x10x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x100x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x10000x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x10x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x10x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x10x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x1000x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x10000x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x100x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x10000x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x100x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x10x0.100_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x10000x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/100x10x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x1000x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x1000x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x10000x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x10x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x100x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x100x0.010_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x10x0.001_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10000x100x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x10x0.001_bench.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/10x100x0.100_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/bench_tables/1000x10000x0.010_bench_hdf5.biom.gz -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/bench_tables copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/tests/test_parse.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/__init__.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/table.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/_subsample.cpython-311.so -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/util.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/_filter.pyx -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/_transform.cpython-311.so -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/parse.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/_transform.pyx -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom creating /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli/metadata_adder.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli/table_normalizer.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli/__init__.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli/table_converter.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli/installation_informer.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli/table_summarizer.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli/util.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli/table_subsetter.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli/metadata_exporter.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli/uc_processor.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli/table_validator.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli/table_head.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/cli/table_ids.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/err.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom creating /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/assets copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/assets/exercise_cli.sh -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/assets copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/assets/exercise_api.py -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/assets copying build/lib.freebsd-14.3-RELEASE-p1-amd64-cpython-311/biom/_filter.cpython-311.so -> /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/exception.py to exception.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_util.py to test_util.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_err.py to test_err.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli/test_show_install_info.py to test_show_install_info.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli/test_subset_table.py to test_subset_table.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli/test_validate_table.py to test_validate_table.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli/test_uc_processor.py to test_uc_processor.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli/test_table_normalizer.py to test_table_normalizer.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli/test_table_converter.py to test_table_converter.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli/test_add_metadata.py to test_add_metadata.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_cli/test_summarize_table.py to test_summarize_table.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_table.py to test_table.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/long_lines.py to long_lines.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_data/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/tests/test_parse.py to test_parse.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/table.py to table.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/util.py to util.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/parse.py to parse.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli/metadata_adder.py to metadata_adder.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli/table_normalizer.py to table_normalizer.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli/table_converter.py to table_converter.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli/installation_informer.py to installation_informer.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli/table_summarizer.py to table_summarizer.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli/util.py to util.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli/table_subsetter.py to table_subsetter.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli/metadata_exporter.py to metadata_exporter.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli/uc_processor.py to uc_processor.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli/table_validator.py to table_validator.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli/table_head.py to table_head.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/cli/table_ids.py to table_ids.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/err.py to err.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/assets/exercise_api.py to exercise_api.cpython-311.pyc writing byte-compilation script '/tmp/tmpm_z390ni.py' /usr/local/bin/python3.11 /tmp/tmpm_z390ni.py removing /tmp/tmpm_z390ni.py running install_egg_info Copying biom_format.egg-info to /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom_format-2.1.16-py3.11.egg-info running install_scripts Installing biom script to /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/bin writing list of installed files to '/wrkdirs/usr/ports/biology/py-biom-format/work-py311/.PLIST.pymodtmp' /usr/bin/strip /wrkdirs/usr/ports/biology/py-biom-format/work-py311/stage/usr/local/lib/python3.11/site-packages/biom/*.so ===> Creating unique files: Move MAN files needing SUFFIX ===> Creating unique files: Move files needing SUFFIX Move: bin/biom --> bin/biom-3.11 Link: @bin/biom --> bin/biom-3.11 ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-12-15T04:16:43+0000' 'PKG_NOTE_ports_top_git_hash=10f7dee57a4c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=06a08e69f3ac' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for py311-biom-format-2.1.16_1 ===> Building py311-biom-format-2.1.16_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py311-biom-format-2.1.16_1 build of biology/py-biom-format@py311 | py311-biom-format-2.1.16_1 ended at Sun Dec 14 23:18:40 EST 2025 build time: 00:02:00