=>> Building science/py-morphio build started at Wed Jul 8 14:32:23 JST 2026 port directory: /usr/ports/science/py-morphio package name: py312-morphio-3.4.2 building for: FreeBSD s15amd64-setuptools2-job-07 15.1-STABLE FreeBSD 15.1-STABLE 1501501 amd64 maintained by: wen@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 713 Jul 5 18:52 /usr/ports/science/py-morphio/Makefile Ports top last git commit: 18628b9022c9c1c0e7cb5e71c2aa1e1e563ca34a Ports top unclean checkout: yes Port dir last git commit: 3e0fa24d33e9f9bb3f7433a3b07e2e888d1b0043 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.8 Host OSVERSION: 1501501 Jail OSVERSION: 1501501 Job Id: 07 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1501501 UNAME_v=FreeBSD 15.1-STABLE 1501501 UNAME_r=15.1-STABLE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.8 MASTERMNT=/usr/local/poudriere/data/.m/s15amd64-setuptools2/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color GID=0 OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 UID=0 PWD=/usr/local/poudriere/data/.m/s15amd64-setuptools2/07/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=s15amd64-setuptools2 SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/s15amd64-setuptools2/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.8 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py312 MAKE_ARGS= FLAVOR=py312 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- wen@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.12" XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-morphio/work-py312 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-morphio/work-py312 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-morphio/work-py312/.cache HOME=/wrkdirs/usr/ports/science/py-morphio/work-py312 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-morphio/work-py312/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/py-morphio/work-py312/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-morphio/work-py312 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-morphio/work-py312 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-morphio/work-py312/.cache HOME=/wrkdirs/usr/ports/science/py-morphio/work-py312 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-morphio/work-py312/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/py-morphio/work-py312/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python3.12 PYTHON_LIBDIR=lib/python3.12 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=lib/python3.12/site-packages PYTHON_SUFFIX=312 PYTHON_BASESUFFIX=312 PYTHON_TAG=.cpython-312 PYTHON_SOABI=.cpython-312 PYTHON_VER=3.12 PYTHON_BASEVER=3.12 PYTHON_VERSION=python3.12 PYTHON2="@comment " PYTHON3="" OSREL=15.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/morphio" EXAMPLESDIR="share/examples/morphio" DATADIR="share/morphio" WWWDIR="www/morphio" ETCDIR="etc/morphio" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.12 PYTHON_LIBDIR=/usr/local/lib/python3.12 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=/usr/local/lib/python3.12/site-packages PYTHON_SUFFIX=312 PYTHON_BASESUFFIX=312 PYTHON_TAG=.cpython-312 PYTHON_SOABI=.cpython-312 PYTHON_VER=3.12 PYTHON_BASEVER=3.12 PYTHON_VERSION=python3.12 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/morphio DOCSDIR=/usr/local/share/doc/morphio EXAMPLESDIR=/usr/local/share/examples/morphio WWWDIR=/usr/local/www/morphio ETCDIR=/usr/local/etc/morphio --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles OVERLAYS+=/overlays/overlay_setuptools FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### LICENSES_ACCEPTED= EULA ISC MPEG2ENC DEFAULT_VERSIONS+= magick=7 DEFAULT_VERSIONS+= pgsql=18 DEFAULT_VERSIONS+= samba=4.23 DEFAULT_VERSIONS+= ssl=openssl japanese_fcitx5-mozc_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_UNSET= JAWIKI x11_wm_hikari_SET= INPUTMETHOD GAMMA LAYERSHELL SCREENCOPY VIRTUALINPUT X11 .if $(.CURDIR:M*/x11-wm/hikari) WITH_DEBUG= YES .endif #### #### devel_gamin_set= LIBINOTIFY #### Misc Poudriere #### .include "/etc/make.conf.ports_env" DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (kbytes, -y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> License APACHE20 accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py312-morphio-3.4.2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.7.5.pkg [s15amd64-setuptools2-job-07] Installing pkg-2.7.5... [s15amd64-setuptools2-job-07] Extracting pkg-2.7.5: .......... done ===> py312-morphio-3.4.2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py312-morphio-3.4.2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License APACHE20 accepted by the user => morphio-3.4.2.tar.gz doesn't seem to exist in /portdistfiles. => Attempting to fetch https://files.pythonhosted.org/packages/source/m/morphio/morphio-3.4.2.tar.gz morphio-3.4.2.tar.gz 673 kB 31 MBps 00s ===> Fetching all distfiles required by py312-morphio-3.4.2 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License APACHE20 accepted by the user ===> Fetching all distfiles required by py312-morphio-3.4.2 for building => SHA256 Checksum OK for morphio-3.4.2.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 APACHE20 accepted by the user ===> Fetching all distfiles required by py312-morphio-3.4.2 for building ===> Extracting for py312-morphio-3.4.2 => SHA256 Checksum OK for morphio-3.4.2.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 py312-morphio-3.4.2 ===> Applying FreeBSD patches for py312-morphio-3.4.2 from /usr/ports/science/py-morphio/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py312-morphio-3.4.2 depends on package: py312-setuptools>=61.0 - not found ===> Installing existing package /packages/All/py312-setuptools-81.0.0.pkg [s15amd64-setuptools2-job-07] Installing py312-setuptools-81.0.0... [s15amd64-setuptools2-job-07] `-- Installing py312-more-itertools-11.1.0... [s15amd64-setuptools2-job-07] | `-- Installing python312-3.12.13_3... [s15amd64-setuptools2-job-07] | | `-- Installing expat-2.8.2... [s15amd64-setuptools2-job-07] | | `-- Extracting expat-2.8.2: .......... done [s15amd64-setuptools2-job-07] | | `-- Installing gettext-runtime-1.0_1... [s15amd64-setuptools2-job-07] | | `-- Installing indexinfo-0.3.1_1... [s15amd64-setuptools2-job-07] | | `-- Extracting indexinfo-0.3.1_1: .... done [s15amd64-setuptools2-job-07] | | `-- Extracting gettext-runtime-1.0_1: .......... done [s15amd64-setuptools2-job-07] | | `-- Installing libffi-3.6.0... [s15amd64-setuptools2-job-07] | | `-- Extracting libffi-3.6.0: .......... done [s15amd64-setuptools2-job-07] | | `-- Installing mpdecimal-4.0.1... [s15amd64-setuptools2-job-07] | | `-- Extracting mpdecimal-4.0.1: .......... done [s15amd64-setuptools2-job-07] | | `-- Installing openssl-3.0.21,1... [s15amd64-setuptools2-job-07] | | `-- Extracting openssl-3.0.21,1: .......... done [s15amd64-setuptools2-job-07] | | `-- Installing readline-8.3.3... [s15amd64-setuptools2-job-07] | | `-- Extracting readline-8.3.3: .......... done [s15amd64-setuptools2-job-07] | `-- Extracting python312-3.12.13_3: .......... done [s15amd64-setuptools2-job-07] `-- Extracting py312-more-itertools-11.1.0: .......... done [s15amd64-setuptools2-job-07] `-- Installing py312-packaging-26.2... [s15amd64-setuptools2-job-07] `-- Extracting py312-packaging-26.2: .......... done [s15amd64-setuptools2-job-07] `-- Installing py312-wheel-0.47.0... [s15amd64-setuptools2-job-07] `-- Extracting py312-wheel-0.47.0: .......... done [s15amd64-setuptools2-job-07] Extracting py312-setuptools-81.0.0: .......... done ===== Message from openssl-3.0.21,1: -- This port (security/openssl) will update from 3.0 to 3.5 per 2026-07-01 (2026Q3) in anticipation of the End-of-Life of OpenSSL 3.0. A new port (security/openssl30) will be created for the remainder of the lifespan of OpenSSL 3.0 and FreeBSD 14. See: https://openssl-library.org/roadmap/index.html ===== Message from python312-3.12.13_3: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py312-gdbm databases/py-gdbm@py312 py312-sqlite3 databases/py-sqlite3@py312 py312-tkinter x11-toolkits/py-tkinter@py312 ===> py312-morphio-3.4.2 depends on package: py312-setuptools>=61.0 - found ===> Returning to build of py312-morphio-3.4.2 ===> py312-morphio-3.4.2 depends on package: py312-setuptools-scm>0 - not found ===> Installing existing package /packages/All/py312-setuptools-scm-9.2.2.pkg [s15amd64-setuptools2-job-07] Installing py312-setuptools-scm-9.2.2... [s15amd64-setuptools2-job-07] Extracting py312-setuptools-scm-9.2.2: .......... done ===> py312-morphio-3.4.2 depends on package: py312-setuptools-scm>0 - found ===> Returning to build of py312-morphio-3.4.2 ===> py312-morphio-3.4.2 depends on package: py312-wheel>0 - found ===> py312-morphio-3.4.2 depends on executable: cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.12_3.pkg [s15amd64-setuptools2-job-07] Installing cmake-core-3.31.12_3... [s15amd64-setuptools2-job-07] `-- Installing jsoncpp-1.9.6_1... [s15amd64-setuptools2-job-07] `-- Extracting jsoncpp-1.9.6_1: .......... done [s15amd64-setuptools2-job-07] `-- Installing libidn2-2.3.8... [s15amd64-setuptools2-job-07] | `-- Installing libunistring-1.4.2... [s15amd64-setuptools2-job-07] | `-- Extracting libunistring-1.4.2: .......... done [s15amd64-setuptools2-job-07] `-- Extracting libidn2-2.3.8: .......... done [s15amd64-setuptools2-job-07] `-- Installing libuv-1.52.1... [s15amd64-setuptools2-job-07] `-- Extracting libuv-1.52.1: .......... done [s15amd64-setuptools2-job-07] `-- Installing rhash-1.4.6... [s15amd64-setuptools2-job-07] `-- Extracting rhash-1.4.6: .......... done [s15amd64-setuptools2-job-07] Extracting cmake-core-3.31.12_3: .......... done ===> py312-morphio-3.4.2 depends on executable: cmake - found ===> Returning to build of py312-morphio-3.4.2 ===> py312-morphio-3.4.2 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.13.2,4.pkg [s15amd64-setuptools2-job-07] Installing ninja-1.13.2,4... [s15amd64-setuptools2-job-07] Extracting ninja-1.13.2,4: ........ done ===> py312-morphio-3.4.2 depends on executable: ninja - found ===> Returning to build of py312-morphio-3.4.2 ===> py312-morphio-3.4.2 depends on package: pybind11>0 - not found ===> Installing existing package /packages/All/pybind11-3.0.4.pkg [s15amd64-setuptools2-job-07] Installing pybind11-3.0.4... [s15amd64-setuptools2-job-07] Extracting pybind11-3.0.4: .......... done ===> py312-morphio-3.4.2 depends on package: pybind11>0 - found ===> Returning to build of py312-morphio-3.4.2 ===> py312-morphio-3.4.2 depends on file: /usr/local/bin/python3.12 - found ===> py312-morphio-3.4.2 depends on package: py312-build>=0 - not found ===> Installing existing package /packages/All/py312-build-1.5.0.pkg [s15amd64-setuptools2-job-07] Installing py312-build-1.5.0... [s15amd64-setuptools2-job-07] `-- Installing py312-pyproject-hooks-1.2.0... [s15amd64-setuptools2-job-07] `-- Extracting py312-pyproject-hooks-1.2.0: .......... done [s15amd64-setuptools2-job-07] Extracting py312-build-1.5.0: .......... done ===> py312-morphio-3.4.2 depends on package: py312-build>=0 - found ===> Returning to build of py312-morphio-3.4.2 ===> py312-morphio-3.4.2 depends on package: py312-installer>=0 - not found ===> Installing existing package /packages/All/py312-installer-1.0.1.pkg [s15amd64-setuptools2-job-07] Installing py312-installer-1.0.1... [s15amd64-setuptools2-job-07] Extracting py312-installer-1.0.1: .......... done ===> py312-morphio-3.4.2 depends on package: py312-installer>=0 - found ===> Returning to build of py312-morphio-3.4.2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py312-morphio-3.4.2 depends on shared library: libhdf5.so - not found ===> Installing existing package /packages/All/hdf5-1.12.2_2,1.pkg [s15amd64-setuptools2-job-07] Installing hdf5-1.12.2_2,1... [s15amd64-setuptools2-job-07] `-- Installing gcc14-14.2.0_6... [s15amd64-setuptools2-job-07] | `-- Installing binutils-2.44,1... [s15amd64-setuptools2-job-07] | | `-- Installing zstd-1.5.7_2... [s15amd64-setuptools2-job-07] | | `-- Installing liblz4-1.10.0_2,1... [s15amd64-setuptools2-job-07] | | `-- Extracting liblz4-1.10.0_2,1: .......... done [s15amd64-setuptools2-job-07] | | `-- Extracting zstd-1.5.7_2: .......... done [s15amd64-setuptools2-job-07] | `-- Extracting binutils-2.44,1: .......... done [s15amd64-setuptools2-job-07] | `-- Installing gmp-6.3.0... [s15amd64-setuptools2-job-07] | `-- Extracting gmp-6.3.0: .......... done [s15amd64-setuptools2-job-07] | `-- Installing mpc-1.4.1... [s15amd64-setuptools2-job-07] | | `-- Installing mpfr-4.2.2,1... [s15amd64-setuptools2-job-07] | | `-- Extracting mpfr-4.2.2,1: .......... done [s15amd64-setuptools2-job-07] | `-- Extracting mpc-1.4.1: .......... done [s15amd64-setuptools2-job-07] `-- Extracting gcc14-14.2.0_6: .......... done [s15amd64-setuptools2-job-07] `-- Installing libaec-1.1.7... [s15amd64-setuptools2-job-07] `-- Extracting libaec-1.1.7: .......... done [s15amd64-setuptools2-job-07] Extracting hdf5-1.12.2_2,1: .......... done ===== Message from gcc14-14.2.0_6: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc14 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> py312-morphio-3.4.2 depends on shared library: libhdf5.so - found (/usr/local/lib/libhdf5.so) ===> Returning to build of py312-morphio-3.4.2 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Configuring for py312-morphio-3.4.2 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building for py312-morphio-3.4.2 * Getting build dependencies for wheel... * Building wheel... /usr/local/lib/python3.12/site-packages/setuptools_scm/_integration/version_inference.py:51: UserWarning: version of morphio already set warnings.warn(self.message) running bdist_wheel running build running build_py creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/morphio copying morphio/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/morphio creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/morphio/mut copying morphio/mut/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/morphio/mut creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/morphio/vasculature copying morphio/vasculature/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/morphio/vasculature running build_ext -- The C compiler identification is Clang 21.1.8 -- The CXX compiler identification is Clang 21.1.8 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done Floating Point Type: float -- Found HDF5: hdf5-shared (found version "1.12.2") -- Project 'gsl-lite', version: '1.0.1' CMake Deprecation Warning at 3rdparty/ghc_filesystem/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- System name: FreeBSD -- Compiler ID: Clang -- CMAKE_CXX_COMPILE_FEATURES: cxx_std_98;cxx_template_template_parameters;cxx_std_11;cxx_alias_templates;cxx_alignas;cxx_alignof;cxx_attributes;cxx_auto_type;cxx_constexpr;cxx_decltype;cxx_decltype_incomplete_return_types;cxx_default_function_template_args;cxx_defaulted_functions;cxx_defaulted_move_initializers;cxx_delegating_constructors;cxx_deleted_functions;cxx_enum_forward_declarations;cxx_explicit_conversions;cxx_extended_friend_declarations;cxx_extern_templates;cxx_final;cxx_func_identifier;cxx_generalized_initializers;cxx_inheriting_constructors;cxx_inline_namespaces;cxx_lambdas;cxx_local_type_template_args;cxx_long_long_type;cxx_noexcept;cxx_nonstatic_member_init;cxx_nullptr;cxx_override;cxx_range_for;cxx_raw_string_literals;cxx_reference_qualified_functions;cxx_right_angle_brackets;cxx_rvalue_references;cxx_sizeof_member;cxx_static_assert;cxx_strong_enums;cxx_thread_local;cxx_trailing_return_types;cxx_unicode_literals;cxx_uniform_initialization;cxx_unrestricted_unions;cxx_user_literals;cxx_variadic_macros;cxx_variadic_templates;cxx_std_14;cxx_aggregate_default_initializers;cxx_attribute_deprecated;cxx_binary_literals;cxx_contextual_conversions;cxx_decltype_auto;cxx_digit_separators;cxx_generic_lambdas;cxx_lambda_init_captures;cxx_relaxed_constexpr;cxx_return_type_deduction;cxx_variable_templates;cxx_std_17;cxx_std_20;cxx_std_23;cxx_std_26 -- pybind11 v3.0.1 -- Found Python: /usr/local/bin/python3.12 (found suitable version "3.12.13", minimum required is "3.8") found components: Interpreter Development.Module Development.Embed Using compatibility mode for Python, set PYBIND11_FINDPYTHON to NEW/OLD to silence this message -- Performing Test HAS_FLTO_THIN -- Performing Test HAS_FLTO_THIN - Success -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Configuring done (1.4s) -- Generating done (0.0s) -- Build files have been written to: /wrkdirs/usr/ports/science/py-morphio/work-py312/morphio-3.4.2/build/temp.freebsd-15.1-STABLE-amd64-cpython-312 [1/48] Building CXX object src/CMakeFiles/morphio_obj.dir/endoplasmic_reticulum.cpp.o [2/48] Building CXX object src/CMakeFiles/morphio_obj.dir/enums.cpp.o [3/48] Building CXX object src/CMakeFiles/morphio_obj.dir/errorMessages.cpp.o [4/48] Building CXX object src/CMakeFiles/morphio_obj.dir/point_utils.cpp.o [5/48] Building CXX object src/CMakeFiles/morphio_obj.dir/mut/endoplasmic_reticulum.cpp.o [6/48] Building CXX object src/CMakeFiles/morphio_obj.dir/mut/soma.cpp.o [7/48] Building CXX object src/CMakeFiles/morphio_obj.dir/properties.cpp.o [8/48] Building CXX object src/CMakeFiles/morphio_obj.dir/readers/utils.cpp.o [9/48] Building CXX object src/CMakeFiles/morphio_obj.dir/glial_cell.cpp.o [10/48] Building CXX object src/CMakeFiles/morphio_obj.dir/collection.cpp.o [11/48] Building CXX object src/CMakeFiles/morphio_obj.dir/error_message_generation.cpp.o [12/48] Building CXX object src/CMakeFiles/morphio_obj.dir/mito_section.cpp.o [13/48] Building CXX object src/CMakeFiles/morphio_obj.dir/mitochondria.cpp.o [14/48] Building CXX object src/CMakeFiles/morphio_obj.dir/mut/dendritic_spine.cpp.o [15/48] Building CXX object src/CMakeFiles/morphio_obj.dir/mut/glial_cell.cpp.o [16/48] Building CXX object src/CMakeFiles/morphio_obj.dir/mut/morphology.cpp.o [17/48] Building CXX object src/CMakeFiles/morphio_obj.dir/mut/section.cpp.o [18/48] Building CXX object src/CMakeFiles/morphio_obj.dir/mut/writer_asc.cpp.o [19/48] Building CXX object src/CMakeFiles/morphio_obj.dir/mut/writer_hdf5.cpp.o [20/48] Building CXX object src/CMakeFiles/morphio_obj.dir/mut/writer_swc.cpp.o [21/48] Building CXX object src/CMakeFiles/morphio_obj.dir/mut/writer_utils.cpp.o [22/48] Building CXX object src/CMakeFiles/morphio_obj.dir/dendritic_spine.cpp.o [23/48] Building CXX object src/CMakeFiles/morphio_obj.dir/mut/mito_section.cpp.o [24/48] Building CXX object src/CMakeFiles/morphio_obj.dir/mut/mitochondria.cpp.o [25/48] Building CXX object src/CMakeFiles/morphio_obj.dir/mut/modifiers.cpp.o [26/48] Building CXX object src/CMakeFiles/morphio_obj.dir/version.cpp.o [27/48] Building CXX object src/CMakeFiles/morphio_obj.dir/morphology.cpp.o [28/48] Building CXX object src/CMakeFiles/morphio_obj.dir/vasc/properties.cpp.o [29/48] Building CXX object src/CMakeFiles/morphio_obj.dir/vasc/section.cpp.o [30/48] Building CXX object src/CMakeFiles/morphio_obj.dir/soma.cpp.o [31/48] Building CXX object src/CMakeFiles/morphio_obj.dir/section.cpp.o [32/48] Building CXX object src/CMakeFiles/morphio_obj.dir/warning_handling.cpp.o [33/48] Building CXX object src/CMakeFiles/morphio_obj.dir/shared_utils.cpp.o [34/48] Building CXX object src/CMakeFiles/morphio_obj.dir/vasc/vasculature.cpp.o [35/48] Building CXX object src/CMakeFiles/morphio_obj.dir/readers/morphologySWC.cpp.o [36/48] Building CXX object src/CMakeFiles/morphio_obj.dir/readers/vasculatureHDF5.cpp.o [37/48] Building CXX object src/CMakeFiles/morphio_obj.dir/readers/morphologyHDF5.cpp.o [38/48] Building CXX object binds/python/CMakeFiles/_morphio.dir/morphio.cpp.o [39/48] Building CXX object src/CMakeFiles/morphio_obj.dir/readers/morphologyASC.cpp.o [40/48] Linking CXX static library src/libmorphio_static.a [41/48] Building CXX object binds/python/CMakeFiles/_morphio.dir/bindings_utils.cpp.o [42/48] Building CXX object binds/python/CMakeFiles/_morphio.dir/bind_enums.cpp.o [43/48] Building CXX object binds/python/CMakeFiles/_morphio.dir/bind_vasculature.cpp.o [44/48] Building CXX object binds/python/CMakeFiles/_morphio.dir/bind_warnings_exceptions.cpp.o [45/48] Building CXX object binds/python/CMakeFiles/_morphio.dir/bind_misc.cpp.o [46/48] Building CXX object binds/python/CMakeFiles/_morphio.dir/bind_immutable.cpp.o [47/48] Building CXX object binds/python/CMakeFiles/_morphio.dir/bind_mutable.cpp.o [48/48] Linking CXX shared module /wrkdirs/usr/ports/science/py-morphio/work-py312/morphio-3.4.2/build/lib.freebsd-15.1-STABLE-amd64-cpython-312/morphio/_morphio.cpython-312.so installing to build/bdist.freebsd-15.1-STABLE-amd64/wheel running install running install_lib creating build/bdist.freebsd-15.1-STABLE-amd64/wheel creating build/bdist.freebsd-15.1-STABLE-amd64/wheel/morphio creating build/bdist.freebsd-15.1-STABLE-amd64/wheel/morphio/vasculature copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/morphio/vasculature/__init__.py -> build/bdist.freebsd-15.1-STABLE-amd64/wheel/./morphio/vasculature creating build/bdist.freebsd-15.1-STABLE-amd64/wheel/morphio/mut copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/morphio/mut/__init__.py -> build/bdist.freebsd-15.1-STABLE-amd64/wheel/./morphio/mut copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/morphio/_morphio.cpython-312.so -> build/bdist.freebsd-15.1-STABLE-amd64/wheel/./morphio copying build/lib.freebsd-15.1-STABLE-amd64-cpython-312/morphio/__init__.py -> build/bdist.freebsd-15.1-STABLE-amd64/wheel/./morphio running install_egg_info running egg_info writing morphio.egg-info/PKG-INFO writing dependency_links to morphio.egg-info/dependency_links.txt writing requirements to morphio.egg-info/requires.txt writing top-level names to morphio.egg-info/top_level.txt reading manifest file 'morphio.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' no previously-included directories found matching 'ci' no previously-included directories found matching 'doc' no previously-included directories found matching 'tests' no previously-included directories found matching 'scripts' no previously-included directories found matching 'examples' adding license file 'LICENSE.txt' adding license file 'AUTHORS.txt' writing manifest file 'morphio.egg-info/SOURCES.txt' Copying morphio.egg-info to build/bdist.freebsd-15.1-STABLE-amd64/wheel/./morphio-3.4.2-py3.12.egg-info running install_scripts creating build/bdist.freebsd-15.1-STABLE-amd64/wheel/morphio-3.4.2.dist-info/WHEEL creating '/wrkdirs/usr/ports/science/py-morphio/work-py312/morphio-3.4.2/dist/.tmp-f2c32fj2/morphio-3.4.2-cp312-cp312-freebsd_15_1_stable_amd64.whl' and adding 'build/bdist.freebsd-15.1-STABLE-amd64/wheel' to it adding 'morphio/__init__.py' adding 'morphio/_morphio.cpython-312.so' adding 'morphio/mut/__init__.py' adding 'morphio/vasculature/__init__.py' adding 'morphio-3.4.2.dist-info/licenses/AUTHORS.txt' adding 'morphio-3.4.2.dist-info/licenses/LICENSE.txt' adding 'morphio-3.4.2.dist-info/METADATA' adding 'morphio-3.4.2.dist-info/WHEEL' adding 'morphio-3.4.2.dist-info/top_level.txt' adding 'morphio-3.4.2.dist-info/RECORD' removing build/bdist.freebsd-15.1-STABLE-amd64/wheel Successfully built morphio-3.4.2-cp312-cp312-freebsd_15_1_stable_amd64.whl =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py312-morphio-3.4.2 depends on file: /usr/local/bin/python3.12 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Staging for py312-morphio-3.4.2 ===> Generating temporary packing list ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2026-07-08T05:32:23+0000' 'PKG_NOTE_ports_top_git_hash=18628b9022c9c1c0e7cb5e71c2aa1e1e563ca34a' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=3e0fa24d33e9f9bb3f7433a3b07e2e888d1b0043' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.8' NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building packages for py312-morphio-3.4.2 ===> Building py312-morphio-3.4.2 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py312-morphio-3.4.2 build of science/py-morphio@py312 | py312-morphio-3.4.2 ended at Wed Jul 8 14:35:02 JST 2026 build time: 00:03:02