=>> Building science/py-rmsd build started at Sun Apr 12 15:41:28 JST 2026 port directory: /usr/ports/science/py-rmsd package name: py311-rmsd-1.6.3_2 building for: FreeBSD s15amd64-sphinx-job-08 15.0-STABLE FreeBSD 15.0-STABLE 1500506 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 796 Apr 11 11:19 /usr/ports/science/py-rmsd/Makefile Ports top last git commit: 2b5202d75c6f2419ddc3a85bcd700cec44fdd0ea Ports top unclean checkout: yes Port dir last git commit: 2b5202d75c6f2419ddc3a85bcd700cec44fdd0ea Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.6 Host OSVERSION: 1500506 Jail OSVERSION: 1500506 Job Id: 08 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500506 UNAME_v=FreeBSD 15.0-STABLE 1500506 UNAME_r=15.0-STABLE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.6 MASTERMNT=/usr/local/poudriere/data/.m/s15amd64-sphinx/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color GID=0 OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 UID=0 PWD=/usr/local/poudriere/data/.m/s15amd64-sphinx/08/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=s15amd64-sphinx SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/s15amd64-sphinx/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.6 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-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-rmsd/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-rmsd/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-rmsd/work-py311/.cache HOME=/wrkdirs/usr/ports/science/py-rmsd/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-rmsd/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/py-rmsd/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/science/py-rmsd/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-rmsd/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-rmsd/work-py311/.cache HOME=/wrkdirs/usr/ports/science/py-rmsd/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-rmsd/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/py-rmsd/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=freebsd15 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=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/py311-rmsd" EXAMPLESDIR="share/examples/py311-rmsd" DATADIR="share/py311-rmsd" WWWDIR="www/py311-rmsd" ETCDIR="etc/py311-rmsd" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd15 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-rmsd DOCSDIR=/usr/local/share/doc/py311-rmsd EXAMPLESDIR=/usr/local/share/examples/py311-rmsd WWWDIR=/usr/local/www/py311-rmsd ETCDIR=/usr/local/etc/py311-rmsd --End SUB_LIST-- ---Begin make.conf--- LICENSES_ACCEPTED= EULA ISC MPEG2ENC DEFAULT_VERSIONS+= magick=7 DEFAULT_VERSIONS+= pgsql=18 DEFAULT_VERSIONS+= samba=4.23 DEFAULT_VERSIONS+= ssl=openssl 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 #### #### LICENSES_ACCEPTED= EULA ISC MPEG2ENC DEFAULT_VERSIONS+= magick=7 DEFAULT_VERSIONS+= pgsql=18 DEFAULT_VERSIONS+= samba=4.23 DEFAULT_VERSIONS+= ssl=openssl japanese_fcitx5-mozc_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_UNSET= JAWIKI x11_wm_hikari_SET= INPUTMETHOD GAMMA LAYERSHELL SCREENCOPY VIRTUALINPUT X11 .if $(.CURDIR:M*/x11-wm/hikari) WITH_DEBUG= YES .endif #### #### DEFAULT_VERSIONS+= ssl=base SET= HTMLDOCS SPHINX BUILD_ALL_PYTHON_FLAVORS= yes #### Misc Poudriere #### .include "/etc/make.conf.ports_env" DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> License BSD2CLAUSE accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-rmsd-1.6.3_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.6.2_1.pkg [s15amd64-sphinx-job-08] Installing pkg-2.6.2_1... [s15amd64-sphinx-job-08] Extracting pkg-2.6.2_1: .......... done ===> py311-rmsd-1.6.3_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py311-rmsd-1.6.3_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD2CLAUSE accepted by the user => charnley-rmsd-rmsd-1.6.3_GH0.tar.gz doesn't seem to exist in /portdistfiles. => Attempting to fetch https://codeload.github.com/charnley/rmsd/tar.gz/rmsd-1.6.3?dummy=/charnley-rmsd-rmsd-1.6.3_GH0.tar.gz fetch: https://codeload.github.com/charnley/rmsd/tar.gz/rmsd-1.6.3?dummy=/charnley-rmsd-rmsd-1.6.3_GH0.tar.gz: size unknown fetch: https://codeload.github.com/charnley/rmsd/tar.gz/rmsd-1.6.3?dummy=/charnley-rmsd-rmsd-1.6.3_GH0.tar.gz: size of remote file is not known charnley-rmsd-rmsd-1.6.3_GH0.tar.gz 243 kB 12 MBps 00s ===> Fetching all distfiles required by py311-rmsd-1.6.3_2 for building =========================================================================== =================================================== ===== env: FETCH_REGET=0 NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by py311-rmsd-1.6.3_2 for building => SHA256 Checksum OK for charnley-rmsd-rmsd-1.6.3_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by py311-rmsd-1.6.3_2 for building ===> Extracting for py311-rmsd-1.6.3_2 => SHA256 Checksum OK for charnley-rmsd-rmsd-1.6.3_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Patching for py311-rmsd-1.6.3_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-rmsd-1.6.3_2 depends on package: py311-setuptools>=63.1.0 - not found ===> Installing existing package /packages/All/py311-setuptools-63.1.0_3.pkg [s15amd64-sphinx-job-08] Installing py311-setuptools-63.1.0_3... [s15amd64-sphinx-job-08] `-- Installing python311-3.11.15_2... [s15amd64-sphinx-job-08] | `-- Installing gettext-runtime-1.0... [s15amd64-sphinx-job-08] | | `-- Installing indexinfo-0.3.1_1... [s15amd64-sphinx-job-08] | | `-- Extracting indexinfo-0.3.1_1: .... done [s15amd64-sphinx-job-08] | `-- Extracting gettext-runtime-1.0: .......... done [s15amd64-sphinx-job-08] | `-- Installing libffi-3.5.1... [s15amd64-sphinx-job-08] | `-- Extracting libffi-3.5.1: .......... done [s15amd64-sphinx-job-08] | `-- Installing mpdecimal-4.0.1... [s15amd64-sphinx-job-08] | `-- Extracting mpdecimal-4.0.1: .......... done [s15amd64-sphinx-job-08] | `-- Installing readline-8.3.3... [s15amd64-sphinx-job-08] | `-- Extracting readline-8.3.3: .......... done [s15amd64-sphinx-job-08] `-- Extracting python311-3.11.15_2: .......... done [s15amd64-sphinx-job-08] Extracting py311-setuptools-63.1.0_3: .......... done ===== Message from python311-3.11.15_2: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> py311-rmsd-1.6.3_2 depends on package: py311-setuptools>=63.1.0 - found ===> Returning to build of py311-rmsd-1.6.3_2 ===> py311-rmsd-1.6.3_2 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Configuring for py311-rmsd-1.6.3_2 /usr/local/lib/python3.11/site-packages/setuptools/config/pyprojecttoml.py:104: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*. warnings.warn(msg, _BetaConfiguration) /usr/local/lib/python3.11/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'entry-points' defined outside of `pyproject.toml` would be ignored. !! ########################################################################## # configuration would be ignored/result in error due to `pyproject.toml` # ########################################################################## The following seems to be defined outside of `pyproject.toml`: `entry-points = {'console_scripts': ['calculate_rmsd=rmsd.calculate_rmsd:main']}` According to the spec (see the link below), however, setuptools CANNOT consider this value unless 'entry-points' is listed as `dynamic`. https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ For the time being, `setuptools` will still consider the given value (as a **transitional** measure), but please note that future releases of setuptools will follow strictly the standard. To prevent this warning, you can list 'entry-points' under `dynamic` or alternatively remove the `[project]` table from your file and rely entirely on other means of configuration. !! warnings.warn(msg, _WouldIgnoreField) running config =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building for py311-rmsd-1.6.3_2 /usr/local/lib/python3.11/site-packages/setuptools/config/pyprojecttoml.py:104: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*. warnings.warn(msg, _BetaConfiguration) /usr/local/lib/python3.11/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'entry-points' defined outside of `pyproject.toml` would be ignored. !! ########################################################################## # configuration would be ignored/result in error due to `pyproject.toml` # ########################################################################## The following seems to be defined outside of `pyproject.toml`: `entry-points = {'console_scripts': ['calculate_rmsd=rmsd.calculate_rmsd:main']}` According to the spec (see the link below), however, setuptools CANNOT consider this value unless 'entry-points' is listed as `dynamic`. https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ For the time being, `setuptools` will still consider the given value (as a **transitional** measure), but please note that future releases of setuptools will follow strictly the standard. To prevent this warning, you can list 'entry-points' under `dynamic` or alternatively remove the `[project]` table from your file and rely entirely on other means of configuration. !! warnings.warn(msg, _WouldIgnoreField) running build running build_py creating build creating build/lib creating build/lib/rmsd copying rmsd/__main__.py -> build/lib/rmsd copying rmsd/__init__.py -> build/lib/rmsd copying rmsd/version.py -> build/lib/rmsd copying rmsd/calculate_rmsd.py -> build/lib/rmsd running egg_info creating rmsd.egg-info writing rmsd.egg-info/PKG-INFO writing dependency_links to rmsd.egg-info/dependency_links.txt writing entry points to rmsd.egg-info/entry_points.txt writing requirements to rmsd.egg-info/requires.txt writing top-level names to rmsd.egg-info/top_level.txt writing manifest file 'rmsd.egg-info/SOURCES.txt' reading manifest file 'rmsd.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'rmsd.egg-info/SOURCES.txt' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-rmsd-1.6.3_2 depends on package: py311-numpy1>=1.16 - not found ===> Installing existing package /packages/All/py311-numpy1-1.26.4_3.pkg [s15amd64-sphinx-job-08] Installing py311-numpy1-1.26.4_3... [s15amd64-sphinx-job-08] `-- Installing gcc14-14.2.0_4... [s15amd64-sphinx-job-08] | `-- Installing binutils-2.44,1... [s15amd64-sphinx-job-08] | | `-- Installing zstd-1.5.7_1... [s15amd64-sphinx-job-08] | | `-- Extracting zstd-1.5.7_1: .......... done [s15amd64-sphinx-job-08] | `-- Extracting binutils-2.44,1: .......... done [s15amd64-sphinx-job-08] | `-- Installing gmp-6.3.0... [s15amd64-sphinx-job-08] | `-- Extracting gmp-6.3.0: .......... done [s15amd64-sphinx-job-08] | `-- Installing mpc-1.4.0... [s15amd64-sphinx-job-08] | | `-- Installing mpfr-4.2.2,1... [s15amd64-sphinx-job-08] | | `-- Extracting mpfr-4.2.2,1: .......... done [s15amd64-sphinx-job-08] | `-- Extracting mpc-1.4.0: .......... done [s15amd64-sphinx-job-08] `-- Extracting gcc14-14.2.0_4: .......... done [s15amd64-sphinx-job-08] `-- Installing openblas-0.3.30,2... [s15amd64-sphinx-job-08] `-- Extracting openblas-0.3.30,2: .......... done [s15amd64-sphinx-job-08] Extracting py311-numpy1-1.26.4_3: .......... 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-rmsd-1.6.3_2 depends on package: py311-numpy1>=1.16 - found ===> Returning to build of py311-rmsd-1.6.3_2 ===> py311-rmsd-1.6.3_2 depends on package: py311-scipy>0 - not found ===> Installing existing package /packages/All/py311-scipy-1.17.1_1,1.pkg [s15amd64-sphinx-job-08] Installing py311-scipy-1.17.1_1,1... [s15amd64-sphinx-job-08] `-- Installing qhull-8.0.2_3,1... [s15amd64-sphinx-job-08] `-- Extracting qhull-8.0.2_3,1: .......... done [s15amd64-sphinx-job-08] Extracting py311-scipy-1.17.1_1,1: .......... done ===> py311-rmsd-1.6.3_2 depends on package: py311-scipy>0 - found ===> Returning to build of py311-rmsd-1.6.3_2 ===> py311-rmsd-1.6.3_2 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Staging for py311-rmsd-1.6.3_2 ===> Generating temporary packing list /usr/local/lib/python3.11/site-packages/setuptools/config/pyprojecttoml.py:104: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*. warnings.warn(msg, _BetaConfiguration) /usr/local/lib/python3.11/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'entry-points' defined outside of `pyproject.toml` would be ignored. !! ########################################################################## # configuration would be ignored/result in error due to `pyproject.toml` # ########################################################################## The following seems to be defined outside of `pyproject.toml`: `entry-points = {'console_scripts': ['calculate_rmsd=rmsd.calculate_rmsd:main']}` According to the spec (see the link below), however, setuptools CANNOT consider this value unless 'entry-points' is listed as `dynamic`. https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ For the time being, `setuptools` will still consider the given value (as a **transitional** measure), but please note that future releases of setuptools will follow strictly the standard. To prevent this warning, you can list 'entry-points' under `dynamic` or alternatively remove the `[project]` table from your file and rely entirely on other means of configuration. !! warnings.warn(msg, _WouldIgnoreField) 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 rmsd.egg-info/PKG-INFO writing dependency_links to rmsd.egg-info/dependency_links.txt writing entry points to rmsd.egg-info/entry_points.txt writing requirements to rmsd.egg-info/requires.txt writing top-level names to rmsd.egg-info/top_level.txt reading manifest file 'rmsd.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'rmsd.egg-info/SOURCES.txt' running install_lib creating /wrkdirs/usr/ports/science/py-rmsd/work-py311/stage/usr/local/lib/python3.11 creating /wrkdirs/usr/ports/science/py-rmsd/work-py311/stage/usr/local/lib/python3.11/site-packages creating /wrkdirs/usr/ports/science/py-rmsd/work-py311/stage/usr/local/lib/python3.11/site-packages/rmsd copying build/lib/rmsd/__main__.py -> /wrkdirs/usr/ports/science/py-rmsd/work-py311/stage/usr/local/lib/python3.11/site-packages/rmsd copying build/lib/rmsd/__init__.py -> /wrkdirs/usr/ports/science/py-rmsd/work-py311/stage/usr/local/lib/python3.11/site-packages/rmsd copying build/lib/rmsd/version.py -> /wrkdirs/usr/ports/science/py-rmsd/work-py311/stage/usr/local/lib/python3.11/site-packages/rmsd copying build/lib/rmsd/calculate_rmsd.py -> /wrkdirs/usr/ports/science/py-rmsd/work-py311/stage/usr/local/lib/python3.11/site-packages/rmsd byte-compiling /wrkdirs/usr/ports/science/py-rmsd/work-py311/stage/usr/local/lib/python3.11/site-packages/rmsd/__main__.py to __main__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-rmsd/work-py311/stage/usr/local/lib/python3.11/site-packages/rmsd/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-rmsd/work-py311/stage/usr/local/lib/python3.11/site-packages/rmsd/version.py to version.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-rmsd/work-py311/stage/usr/local/lib/python3.11/site-packages/rmsd/calculate_rmsd.py to calculate_rmsd.cpython-311.pyc writing byte-compilation script '/tmp/tmpqm51tue_.py' /usr/local/bin/python3.11 /tmp/tmpqm51tue_.py removing /tmp/tmpqm51tue_.py running install_egg_info Copying rmsd.egg-info to /wrkdirs/usr/ports/science/py-rmsd/work-py311/stage/usr/local/lib/python3.11/site-packages/rmsd-1.6.3-py3.11.egg-info running install_scripts Installing calculate_rmsd script to /wrkdirs/usr/ports/science/py-rmsd/work-py311/stage/usr/local/bin writing list of installed files to '/wrkdirs/usr/ports/science/py-rmsd/work-py311/.PLIST.pymodtmp' ===> Creating unique files: Move MAN files needing SUFFIX ===> Creating unique files: Move files needing SUFFIX Move: bin/calculate_rmsd --> bin/calculate_rmsd-3.11 Link: @bin/calculate_rmsd --> bin/calculate_rmsd-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=2026-04-12T06:41:28+0000' 'PKG_NOTE_ports_top_git_hash=2b5202d75c6f2419ddc3a85bcd700cec44fdd0ea' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=2b5202d75c6f2419ddc3a85bcd700cec44fdd0ea' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.6' NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building packages for py311-rmsd-1.6.3_2 ===> Building py311-rmsd-1.6.3_2 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py311-rmsd-1.6.3_2 build of science/py-rmsd@py311 | py311-rmsd-1.6.3_2 ended at Sun Apr 12 15:41:36 JST 2026 build time: 00:00:08