=>> Building biology/py-ont-fast5-api build started at Fri Jan 23 15:47:51 EST 2026 port directory: /usr/ports/biology/py-ont-fast5-api package name: py311-ont-fast5-api-4.0.2_2 building for: FreeBSD pkg.DaveG.ca 13.5-RELEASE-p7 FreeBSD 13.5-RELEASE-p7 1305000 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1194 Mar 10 2025 /usr/ports/biology/py-ont-fast5-api/Makefile Ports top last git commit: 076a295eb33c 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: 1305000 Job Id: 15 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1305000 UNAME_v=FreeBSD 13.5-RELEASE-p7 1305000 UNAME_r=13.5-RELEASE-p7 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_13_5_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_13_5_x64-HEAD-ALL/15/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_13_5_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_13_5_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-- jwb@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-ont-fast5-api/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-ont-fast5-api/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-ont-fast5-api/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-ont-fast5-api/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-ont-fast5-api/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-ont-fast5-api/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=freebsd13 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=13.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/py311-ont-fast5-api" EXAMPLESDIR="share/examples/py311-ont-fast5-api" DATADIR="share/py311-ont-fast5-api" WWWDIR="www/py311-ont-fast5-api" ETCDIR="etc/py311-ont-fast5-api" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd13 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-ont-fast5-api DOCSDIR=/usr/local/share/doc/py311-ont-fast5-api EXAMPLESDIR=/usr/local/share/examples/py311-ont-fast5-api WWWDIR=/usr/local/www/py311-ont-fast5-api ETCDIR=/usr/local/etc/py311-ont-fast5-api --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 --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-ont-fast5-api-4.0.2_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.5.1.pkg [pkg.DaveG.ca] Installing pkg-2.5.1... [pkg.DaveG.ca] Extracting pkg-2.5.1: .......... done ===> py311-ont-fast5-api-4.0.2_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py311-ont-fast5-api-4.0.2_2 =========================================================================== =================================================== ===== 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-ont-fast5-api-4.0.2_2 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py311-ont-fast5-api-4.0.2_2 for building => SHA256 Checksum OK for nanoporetech-ont_fast5_api-release_4.0.2_GH0.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-ont-fast5-api-4.0.2_2 for building ===> Extracting for py311-ont-fast5-api-4.0.2_2 => SHA256 Checksum OK for nanoporetech-ont_fast5_api-release_4.0.2_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for py311-ont-fast5-api-4.0.2_2 ===> Applying FreeBSD patches for py311-ont-fast5-api-4.0.2_2 from /usr/ports/biology/py-ont-fast5-api/files /bin/rm -f /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/ont_fast5_api-release_4.0.2/ont_fast5_api/vbz_plugin/* =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-ont-fast5-api-4.0.2_2 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] `-- Installing python311-3.11.14... [pkg.DaveG.ca] | `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | `-- Extracting gettext-runtime-0.26: .......... 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-8.3.3... [pkg.DaveG.ca] | `-- Extracting readline-8.3.3: .......... done [pkg.DaveG.ca] `-- Extracting python311-3.11.14: .......... done [pkg.DaveG.ca] Extracting py311-setuptools-63.1.0_3: .......... done ===== Message from python311-3.11.14: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> py311-ont-fast5-api-4.0.2_2 depends on package: py311-setuptools>=63.1.0 - found ===> Returning to build of py311-ont-fast5-api-4.0.2_2 ===> py311-ont-fast5-api-4.0.2_2 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-ont-fast5-api-4.0.2_2 depends on shared library: libvbz_hdf_plugin.so - not found ===> Installing existing package /packages/All/vbz-compression-1.0.13.pkg [pkg.DaveG.ca] Installing vbz-compression-1.0.13... [pkg.DaveG.ca] `-- Installing hdf5-1.12.2_2,1... [pkg.DaveG.ca] | `-- Installing gcc14-14.2.0_4... [pkg.DaveG.ca] | | `-- Installing binutils-2.44,1... [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 gcc14-14.2.0_4: .......... done [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 vbz-compression-1.0.13: .. done ===== Message from gcc14-14.2.0_4: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc14 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> py311-ont-fast5-api-4.0.2_2 depends on shared library: libvbz_hdf_plugin.so - found (/usr/local/hdf5/lib/plugin/libvbz_hdf_plugin.so) ===> Returning to build of py311-ont-fast5-api-4.0.2_2 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for py311-ont-fast5-api-4.0.2_2 running config =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-ont-fast5-api-4.0.2_2 depends on package: py311-numpy>=1.16,1<1.27,1 - not found ===> Installing existing package /packages/All/py311-numpy-1.26.4_12,1.pkg [pkg.DaveG.ca] Installing py311-numpy-1.26.4_12,1... [pkg.DaveG.ca] `-- Installing openblas-0.3.30,2... [pkg.DaveG.ca] `-- Extracting openblas-0.3.30,2: .......... 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_12,1: .......... done ===> py311-ont-fast5-api-4.0.2_2 depends on package: py311-numpy>=1.16,1<1.27,1 - found ===> Returning to build of py311-ont-fast5-api-4.0.2_2 ===> py311-ont-fast5-api-4.0.2_2 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] Extracting py311-h5py-3.15.1: .......... done ===> py311-ont-fast5-api-4.0.2_2 depends on package: py311-h5py>=2.2.0 - found ===> Returning to build of py311-ont-fast5-api-4.0.2_2 ===> py311-ont-fast5-api-4.0.2_2 depends on package: py311-six>0 - not found ===> Installing existing package /packages/All/py311-six-1.17.0.pkg [pkg.DaveG.ca] Installing py311-six-1.17.0... [pkg.DaveG.ca] Extracting py311-six-1.17.0: ........ done ===> py311-ont-fast5-api-4.0.2_2 depends on package: py311-six>0 - found ===> Returning to build of py311-ont-fast5-api-4.0.2_2 ===> py311-ont-fast5-api-4.0.2_2 depends on package: py311-progressbar>0 - not found ===> Installing existing package /packages/All/py311-progressbar-2.5_1.pkg [pkg.DaveG.ca] Installing py311-progressbar-2.5_1... [pkg.DaveG.ca] Extracting py311-progressbar-2.5_1: .......... done ===> py311-ont-fast5-api-4.0.2_2 depends on package: py311-progressbar>0 - found ===> Returning to build of py311-ont-fast5-api-4.0.2_2 ===> py311-ont-fast5-api-4.0.2_2 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for py311-ont-fast5-api-4.0.2_2 ===> 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 creating build creating build/lib creating build/lib/ont_fast5_api copying ont_fast5_api/helpers.py -> build/lib/ont_fast5_api copying ont_fast5_api/multi_fast5.py -> build/lib/ont_fast5_api copying ont_fast5_api/static_data.py -> build/lib/ont_fast5_api copying ont_fast5_api/compression_settings.py -> build/lib/ont_fast5_api copying ont_fast5_api/fast5_read.py -> build/lib/ont_fast5_api copying ont_fast5_api/__init__.py -> build/lib/ont_fast5_api copying ont_fast5_api/fast5_info.py -> build/lib/ont_fast5_api copying ont_fast5_api/fast5_file.py -> build/lib/ont_fast5_api copying ont_fast5_api/fast5_interface.py -> build/lib/ont_fast5_api copying ont_fast5_api/data_sanitisation.py -> build/lib/ont_fast5_api creating build/lib/ont_fast5_api/analysis_tools copying ont_fast5_api/analysis_tools/basecall_1d.py -> build/lib/ont_fast5_api/analysis_tools copying ont_fast5_api/analysis_tools/basecall_2d.py -> build/lib/ont_fast5_api/analysis_tools copying ont_fast5_api/analysis_tools/__init__.py -> build/lib/ont_fast5_api/analysis_tools copying ont_fast5_api/analysis_tools/base_tool.py -> build/lib/ont_fast5_api/analysis_tools copying ont_fast5_api/analysis_tools/segmentation.py -> build/lib/ont_fast5_api/analysis_tools copying ont_fast5_api/analysis_tools/event_detection.py -> build/lib/ont_fast5_api/analysis_tools copying ont_fast5_api/analysis_tools/alignment.py -> build/lib/ont_fast5_api/analysis_tools creating build/lib/ont_fast5_api/conversion_tools copying ont_fast5_api/conversion_tools/demux_fast5.py -> build/lib/ont_fast5_api/conversion_tools copying ont_fast5_api/conversion_tools/conversion_utils.py -> build/lib/ont_fast5_api/conversion_tools copying ont_fast5_api/conversion_tools/compress_fast5.py -> build/lib/ont_fast5_api/conversion_tools copying ont_fast5_api/conversion_tools/single_to_multi_fast5.py -> build/lib/ont_fast5_api/conversion_tools copying ont_fast5_api/conversion_tools/__init__.py -> build/lib/ont_fast5_api/conversion_tools copying ont_fast5_api/conversion_tools/fast5_subset.py -> build/lib/ont_fast5_api/conversion_tools copying ont_fast5_api/conversion_tools/multi_to_single_fast5.py -> build/lib/ont_fast5_api/conversion_tools copying ont_fast5_api/conversion_tools/check_file_compression.py -> build/lib/ont_fast5_api/conversion_tools running install_lib creating /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11 creating /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages creating /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api copying build/lib/ont_fast5_api/helpers.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api copying build/lib/ont_fast5_api/multi_fast5.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api copying build/lib/ont_fast5_api/static_data.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api copying build/lib/ont_fast5_api/compression_settings.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api copying build/lib/ont_fast5_api/fast5_read.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api creating /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/analysis_tools copying build/lib/ont_fast5_api/analysis_tools/basecall_1d.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/analysis_tools copying build/lib/ont_fast5_api/analysis_tools/basecall_2d.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/analysis_tools copying build/lib/ont_fast5_api/analysis_tools/__init__.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/analysis_tools copying build/lib/ont_fast5_api/analysis_tools/base_tool.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/analysis_tools copying build/lib/ont_fast5_api/analysis_tools/segmentation.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/analysis_tools copying build/lib/ont_fast5_api/analysis_tools/event_detection.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/analysis_tools copying build/lib/ont_fast5_api/analysis_tools/alignment.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/analysis_tools copying build/lib/ont_fast5_api/__init__.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api copying build/lib/ont_fast5_api/fast5_info.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api copying build/lib/ont_fast5_api/fast5_file.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api copying build/lib/ont_fast5_api/fast5_interface.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api creating /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/conversion_tools copying build/lib/ont_fast5_api/conversion_tools/demux_fast5.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/conversion_tools copying build/lib/ont_fast5_api/conversion_tools/conversion_utils.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/conversion_tools copying build/lib/ont_fast5_api/conversion_tools/compress_fast5.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/conversion_tools copying build/lib/ont_fast5_api/conversion_tools/single_to_multi_fast5.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/conversion_tools copying build/lib/ont_fast5_api/conversion_tools/__init__.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/conversion_tools copying build/lib/ont_fast5_api/conversion_tools/fast5_subset.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/conversion_tools copying build/lib/ont_fast5_api/conversion_tools/multi_to_single_fast5.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/conversion_tools copying build/lib/ont_fast5_api/conversion_tools/check_file_compression.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/conversion_tools copying build/lib/ont_fast5_api/data_sanitisation.py -> /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/helpers.py to helpers.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/multi_fast5.py to multi_fast5.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/static_data.py to static_data.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/compression_settings.py to compression_settings.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/fast5_read.py to fast5_read.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/analysis_tools/basecall_1d.py to basecall_1d.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/analysis_tools/basecall_2d.py to basecall_2d.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/analysis_tools/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/analysis_tools/base_tool.py to base_tool.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/analysis_tools/segmentation.py to segmentation.cpython-311.pyc /usr/local/lib/python3.11/site-packages/ont_fast5_api/analysis_tools/segmentation.py:92: SyntaxWarning: "is" with a literal. Did you mean "=="? byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/analysis_tools/event_detection.py to event_detection.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/analysis_tools/alignment.py to alignment.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/fast5_info.py to fast5_info.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/fast5_file.py to fast5_file.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/fast5_interface.py to fast5_interface.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/conversion_tools/demux_fast5.py to demux_fast5.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/conversion_tools/conversion_utils.py to conversion_utils.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/conversion_tools/compress_fast5.py to compress_fast5.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/conversion_tools/single_to_multi_fast5.py to single_to_multi_fast5.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/conversion_tools/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/conversion_tools/fast5_subset.py to fast5_subset.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/conversion_tools/multi_to_single_fast5.py to multi_to_single_fast5.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/conversion_tools/check_file_compression.py to check_file_compression.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api/data_sanitisation.py to data_sanitisation.cpython-311.pyc writing byte-compilation script '/tmp/tmprbah97dj.py' /usr/local/bin/python3.11 /tmp/tmprbah97dj.py /usr/local/lib/python3.11/site-packages/ont_fast5_api/analysis_tools/segmentation.py:92: SyntaxWarning: "is" with a literal. Did you mean "=="? removing /tmp/tmprbah97dj.py running install_egg_info running egg_info creating ont_fast5_api.egg-info writing ont_fast5_api.egg-info/PKG-INFO writing dependency_links to ont_fast5_api.egg-info/dependency_links.txt writing entry points to ont_fast5_api.egg-info/entry_points.txt writing requirements to ont_fast5_api.egg-info/requires.txt writing top-level names to ont_fast5_api.egg-info/top_level.txt writing manifest file 'ont_fast5_api.egg-info/SOURCES.txt' reading manifest file 'ont_fast5_api.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'README.md' no previously-included directories found matching 'build' no previously-included directories found matching 'docs' adding license file 'LICENSE.md' writing manifest file 'ont_fast5_api.egg-info/SOURCES.txt' Copying ont_fast5_api.egg-info to /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/lib/python3.11/site-packages/ont_fast5_api-4.0.1-py3.11.egg-info running install_scripts Installing check_compression script to /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/bin Installing compress_fast5 script to /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/bin Installing demux_fast5 script to /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/bin Installing fast5_subset script to /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/bin Installing multi_to_single_fast5 script to /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/bin Installing single_to_multi_fast5 script to /wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/stage/usr/local/bin writing list of installed files to '/wrkdirs/usr/ports/biology/py-ont-fast5-api/work-py311/.PLIST.pymodtmp' ===> Creating unique files: Move MAN files needing SUFFIX ===> Creating unique files: Move files needing SUFFIX Move: bin/check_compression --> bin/check_compression-3.11 Link: @bin/check_compression --> bin/check_compression-3.11 Move: bin/compress_fast5 --> bin/compress_fast5-3.11 Link: @bin/compress_fast5 --> bin/compress_fast5-3.11 Move: bin/demux_fast5 --> bin/demux_fast5-3.11 Link: @bin/demux_fast5 --> bin/demux_fast5-3.11 Move: bin/fast5_subset --> bin/fast5_subset-3.11 Link: @bin/fast5_subset --> bin/fast5_subset-3.11 Move: bin/multi_to_single_fast5 --> bin/multi_to_single_fast5-3.11 Link: @bin/multi_to_single_fast5 --> bin/multi_to_single_fast5-3.11 Move: bin/single_to_multi_fast5 --> bin/single_to_multi_fast5-3.11 Link: @bin/single_to_multi_fast5 --> bin/single_to_multi_fast5-3.11 ====> 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=2026-01-23T20:47:51+0000' 'PKG_NOTE_ports_top_git_hash=076a295eb33c' '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-ont-fast5-api-4.0.2_2 ===> Building py311-ont-fast5-api-4.0.2_2 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py311-ont-fast5-api-4.0.2_2 build of biology/py-ont-fast5-api@py311 | py311-ont-fast5-api-4.0.2_2 ended at Fri Jan 23 15:48:21 EST 2026 build time: 00:00:34