=>> Building biology/py-resdk build started at Sat Dec 14 14:13:30 EST 2024 port directory: /usr/ports/biology/py-resdk package name: py311-resdk-21.2.1 building for: FreeBSD ghostbsd-14-ghostbsd_ports-job-24 14.1-STABLE FreeBSD 14.1-STABLE 1401502 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1722 Nov 19 12:01 /usr/ports/biology/py-resdk/Makefile Ports top last git commit: b4bf4e75f8c6 Ports top unclean checkout: no Port dir last git commit: 335c5d9d8a83 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.1_1 Host OSVERSION: 1401501 Jail OSVERSION: 1401502 Job Id: 24 !!! Jail is newer than host. (Jail: 1401502, Host: 1401501) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1401502 UNAME_v=FreeBSD 14.1-STABLE 1401502 UNAME_r=14.1-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=3.4.1_1 MASTERMNT=/zroot/poudriere/data/.m/ghostbsd-14-ghostbsd_ports/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=su GID=0 OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 UID=0 PWD=/zroot/poudriere/data/.m/ghostbsd-14-ghostbsd_ports/24/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=ghostbsd-14-ghostbsd_ports SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/zroot/poudriere/data/.m/ghostbsd-14-ghostbsd_ports/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.1_1 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/biology/py-resdk/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-resdk/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-resdk/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-resdk/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-resdk/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-resdk/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-resdk/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-resdk/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-resdk/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-resdk/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-resdk/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-resdk/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 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " 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_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=14.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/resdk" EXAMPLESDIR="share/examples/resdk" DATADIR="share/resdk" WWWDIR="www/resdk" ETCDIR="etc/resdk" --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_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/resdk DOCSDIR=/usr/local/share/doc/resdk EXAMPLESDIR=/usr/local/share/examples/resdk WWWDIR=/usr/local/www/resdk ETCDIR=/usr/local/etc/resdk --End SUB_LIST-- ---Begin make.conf--- 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 #### Misc Poudriere #### .include "/etc/make.conf.ports_env" ---End make.conf--- --Resource limits-- ulimit: can't get limit: Invalid argument 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=nobody UID=65534 GID=65534 ===> License APACHE20 accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-resdk-21.2.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.21.3.pkg [ghostbsd-14-ghostbsd_ports-job-24] Installing pkg-1.21.3... [ghostbsd-14-ghostbsd_ports-job-24] Extracting pkg-1.21.3: .......... done ===> py311-resdk-21.2.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py311-resdk-21.2.1 =========================================================================== =================================================== ===== 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 ===> Fetching all distfiles required by py311-resdk-21.2.1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License APACHE20 accepted by the user ===> Fetching all distfiles required by py311-resdk-21.2.1 for building => SHA256 Checksum OK for resdk-21.2.1.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 py311-resdk-21.2.1 for building ===> Extracting for py311-resdk-21.2.1 => SHA256 Checksum OK for resdk-21.2.1.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-resdk-21.2.1 ===> Applying FreeBSD patches for py311-resdk-21.2.1 from /usr/ports/biology/py-resdk/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-resdk-21.2.1 depends on package: py311-setuptools>0 - not found ===> Installing existing package /packages/All/py311-setuptools-63.1.0_1.pkg [ghostbsd-14-ghostbsd_ports-job-24] Installing py311-setuptools-63.1.0_1... [ghostbsd-14-ghostbsd_ports-job-24] `-- Installing python311-3.11.11... [ghostbsd-14-ghostbsd_ports-job-24] | `-- Installing gettext-runtime-0.22.5... [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Installing indexinfo-0.3.1... [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Extracting indexinfo-0.3.1: .... done [ghostbsd-14-ghostbsd_ports-job-24] | `-- Extracting gettext-runtime-0.22.5: .......... done [ghostbsd-14-ghostbsd_ports-job-24] | `-- Installing libffi-3.4.6... [ghostbsd-14-ghostbsd_ports-job-24] | `-- Extracting libffi-3.4.6: .......... done [ghostbsd-14-ghostbsd_ports-job-24] | `-- Installing mpdecimal-4.0.0... [ghostbsd-14-ghostbsd_ports-job-24] | `-- Extracting mpdecimal-4.0.0: .......... done [ghostbsd-14-ghostbsd_ports-job-24] | `-- Installing readline-8.2.13_2... [ghostbsd-14-ghostbsd_ports-job-24] | `-- Extracting readline-8.2.13_2: .......... done [ghostbsd-14-ghostbsd_ports-job-24] `-- Extracting python311-3.11.11: .......... done [ghostbsd-14-ghostbsd_ports-job-24] Extracting py311-setuptools-63.1.0_1: .......... done ===== Message from python311-3.11.11: -- 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-resdk-21.2.1 depends on package: py311-setuptools>0 - found ===> Returning to build of py311-resdk-21.2.1 ===> py311-resdk-21.2.1 depends on package: py311-setuptools-scm>=6.4.0 - not found ===> Installing existing package /packages/All/py311-setuptools-scm-8.0.4.pkg [ghostbsd-14-ghostbsd_ports-job-24] Installing py311-setuptools-scm-8.0.4... [ghostbsd-14-ghostbsd_ports-job-24] `-- Installing py311-packaging-24.2... [ghostbsd-14-ghostbsd_ports-job-24] `-- Extracting py311-packaging-24.2: .......... done [ghostbsd-14-ghostbsd_ports-job-24] `-- Installing py311-typing-extensions-4.12.2... [ghostbsd-14-ghostbsd_ports-job-24] `-- Extracting py311-typing-extensions-4.12.2: .......... done [ghostbsd-14-ghostbsd_ports-job-24] Extracting py311-setuptools-scm-8.0.4: .......... done ===> py311-resdk-21.2.1 depends on package: py311-setuptools-scm>=6.4.0 - found ===> Returning to build of py311-resdk-21.2.1 ===> py311-resdk-21.2.1 depends on package: py311-wheel>0 - not found ===> Installing existing package /packages/All/py311-wheel-0.45.1.pkg [ghostbsd-14-ghostbsd_ports-job-24] Installing py311-wheel-0.45.1... [ghostbsd-14-ghostbsd_ports-job-24] Extracting py311-wheel-0.45.1: .......... done ===> py311-resdk-21.2.1 depends on package: py311-wheel>0 - found ===> Returning to build of py311-resdk-21.2.1 ===> py311-resdk-21.2.1 depends on file: /usr/local/bin/python3.11 - found ===> py311-resdk-21.2.1 depends on package: py311-build>=0 - not found ===> Installing existing package /packages/All/py311-build-1.2.2_2.pkg [ghostbsd-14-ghostbsd_ports-job-24] Installing py311-build-1.2.2_2... [ghostbsd-14-ghostbsd_ports-job-24] `-- Installing py311-pyproject-hooks-1.2.0... [ghostbsd-14-ghostbsd_ports-job-24] `-- Extracting py311-pyproject-hooks-1.2.0: .......... done [ghostbsd-14-ghostbsd_ports-job-24] Extracting py311-build-1.2.2_2: .......... done ===> py311-resdk-21.2.1 depends on package: py311-build>=0 - found ===> Returning to build of py311-resdk-21.2.1 ===> py311-resdk-21.2.1 depends on package: py311-installer>=0 - not found ===> Installing existing package /packages/All/py311-installer-0.7.0.pkg [ghostbsd-14-ghostbsd_ports-job-24] Installing py311-installer-0.7.0... [ghostbsd-14-ghostbsd_ports-job-24] Extracting py311-installer-0.7.0: .......... done ===> py311-resdk-21.2.1 depends on package: py311-installer>=0 - found ===> Returning to build of py311-resdk-21.2.1 =========================================================================== =================================================== ===== 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-resdk-21.2.1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building for py311-resdk-21.2.1 * Getting build dependencies for wheel... running egg_info writing src/resdk.egg-info/PKG-INFO writing dependency_links to src/resdk.egg-info/dependency_links.txt writing requirements to src/resdk.egg-info/requires.txt writing top-level names to src/resdk.egg-info/top_level.txt reading manifest file 'src/resdk.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '*' found under directory 'e2e' adding license file 'LICENSE' writing manifest file 'src/resdk.egg-info/SOURCES.txt' * Building wheel... running bdist_wheel running build running build_py creating build creating build/lib creating build/lib/resdk copying src/resdk/resdk_logger.py -> build/lib/resdk copying src/resdk/resolwe.py -> build/lib/resdk copying src/resdk/__init__.py -> build/lib/resdk copying src/resdk/constants.py -> build/lib/resdk copying src/resdk/query.py -> build/lib/resdk copying src/resdk/uploader.py -> build/lib/resdk copying src/resdk/exceptions.py -> build/lib/resdk creating build/lib/resdk/aws copying src/resdk/aws/__init__.py -> build/lib/resdk/aws copying src/resdk/aws/session.py -> build/lib/resdk/aws creating build/lib/resdk/tables copying src/resdk/tables/__init__.py -> build/lib/resdk/tables copying src/resdk/tables/variant.py -> build/lib/resdk/tables copying src/resdk/tables/base.py -> build/lib/resdk/tables copying src/resdk/tables/microarray.py -> build/lib/resdk/tables copying src/resdk/tables/ml_ready.py -> build/lib/resdk/tables copying src/resdk/tables/rna.py -> build/lib/resdk/tables copying src/resdk/tables/methylation.py -> build/lib/resdk/tables copying src/resdk/tables/utils.py -> build/lib/resdk/tables creating build/lib/resdk/shortcuts copying src/resdk/shortcuts/__init__.py -> build/lib/resdk/shortcuts copying src/resdk/shortcuts/collection.py -> build/lib/resdk/shortcuts copying src/resdk/shortcuts/sample.py -> build/lib/resdk/shortcuts creating build/lib/resdk/utils copying src/resdk/utils/decorators.py -> build/lib/resdk/utils copying src/resdk/utils/table_cache.py -> build/lib/resdk/utils copying src/resdk/utils/__init__.py -> build/lib/resdk/utils creating build/lib/resdk/resources copying src/resdk/resources/metadata.py -> build/lib/resdk/resources copying src/resdk/resources/permissions.py -> build/lib/resdk/resources copying src/resdk/resources/annotations.py -> build/lib/resdk/resources copying src/resdk/resources/geneset.py -> build/lib/resdk/resources copying src/resdk/resources/descriptor.py -> build/lib/resdk/resources copying src/resdk/resources/__init__.py -> build/lib/resdk/resources copying src/resdk/resources/base.py -> build/lib/resdk/resources copying src/resdk/resources/background_task.py -> build/lib/resdk/resources copying src/resdk/resources/user.py -> build/lib/resdk/resources copying src/resdk/resources/data.py -> build/lib/resdk/resources copying src/resdk/resources/utils.py -> build/lib/resdk/resources copying src/resdk/resources/collection.py -> build/lib/resdk/resources copying src/resdk/resources/process.py -> build/lib/resdk/resources copying src/resdk/resources/sample.py -> build/lib/resdk/resources copying src/resdk/resources/relation.py -> build/lib/resdk/resources creating build/lib/resdk/resources/kb copying src/resdk/resources/kb/__init__.py -> build/lib/resdk/resources/kb copying src/resdk/resources/kb/mapping.py -> build/lib/resdk/resources/kb copying src/resdk/resources/kb/feature.py -> build/lib/resdk/resources/kb running egg_info writing src/resdk.egg-info/PKG-INFO writing dependency_links to src/resdk.egg-info/dependency_links.txt writing requirements to src/resdk.egg-info/requires.txt writing top-level names to src/resdk.egg-info/top_level.txt reading manifest file 'src/resdk.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '*' found under directory 'e2e' adding license file 'LICENSE' writing manifest file 'src/resdk.egg-info/SOURCES.txt' installing to build/bdist.freebsd-14.1-STABLE-amd64/wheel running install running install_lib creating build/bdist.freebsd-14.1-STABLE-amd64 creating build/bdist.freebsd-14.1-STABLE-amd64/wheel creating build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk creating build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/aws copying build/lib/resdk/aws/__init__.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/aws copying build/lib/resdk/aws/session.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/aws copying build/lib/resdk/resdk_logger.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk copying build/lib/resdk/resolwe.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk copying build/lib/resdk/__init__.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk creating build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/tables copying build/lib/resdk/tables/__init__.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/tables copying build/lib/resdk/tables/variant.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/tables copying build/lib/resdk/tables/base.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/tables copying build/lib/resdk/tables/microarray.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/tables copying build/lib/resdk/tables/ml_ready.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/tables copying build/lib/resdk/tables/rna.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/tables copying build/lib/resdk/tables/methylation.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/tables copying build/lib/resdk/tables/utils.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/tables creating build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/shortcuts copying build/lib/resdk/shortcuts/__init__.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/shortcuts copying build/lib/resdk/shortcuts/collection.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/shortcuts copying build/lib/resdk/shortcuts/sample.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/shortcuts creating build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/utils copying build/lib/resdk/utils/decorators.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/utils copying build/lib/resdk/utils/table_cache.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/utils copying build/lib/resdk/utils/__init__.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/utils copying build/lib/resdk/constants.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk copying build/lib/resdk/query.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk copying build/lib/resdk/uploader.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk copying build/lib/resdk/exceptions.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk creating build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/resources copying build/lib/resdk/resources/metadata.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/resources copying build/lib/resdk/resources/permissions.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/resources copying build/lib/resdk/resources/annotations.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/resources copying build/lib/resdk/resources/geneset.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/resources copying build/lib/resdk/resources/descriptor.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/resources copying build/lib/resdk/resources/__init__.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/resources copying build/lib/resdk/resources/base.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/resources copying build/lib/resdk/resources/background_task.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/resources copying build/lib/resdk/resources/user.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/resources creating build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/resources/kb copying build/lib/resdk/resources/kb/__init__.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/resources/kb copying build/lib/resdk/resources/kb/mapping.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/resources/kb copying build/lib/resdk/resources/kb/feature.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/resources/kb copying build/lib/resdk/resources/data.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/resources copying build/lib/resdk/resources/utils.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/resources copying build/lib/resdk/resources/collection.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/resources copying build/lib/resdk/resources/process.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/resources copying build/lib/resdk/resources/sample.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/resources copying build/lib/resdk/resources/relation.py -> build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk/resources running install_egg_info Copying src/resdk.egg-info to build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk-21.2.1-py3.11.egg-info running install_scripts creating build/bdist.freebsd-14.1-STABLE-amd64/wheel/resdk-21.2.1.dist-info/WHEEL creating '/wrkdirs/usr/ports/biology/py-resdk/work-py311/resdk-21.2.1/dist/tmp0ny5px4k/resdk-21.2.1-py3-none-any.whl' and adding 'build/bdist.freebsd-14.1-STABLE-amd64/wheel' to it adding 'resdk/__init__.py' adding 'resdk/constants.py' adding 'resdk/exceptions.py' adding 'resdk/query.py' adding 'resdk/resdk_logger.py' adding 'resdk/resolwe.py' adding 'resdk/uploader.py' adding 'resdk/aws/__init__.py' adding 'resdk/aws/session.py' adding 'resdk/resources/__init__.py' adding 'resdk/resources/annotations.py' adding 'resdk/resources/background_task.py' adding 'resdk/resources/base.py' adding 'resdk/resources/collection.py' adding 'resdk/resources/data.py' adding 'resdk/resources/descriptor.py' adding 'resdk/resources/geneset.py' adding 'resdk/resources/metadata.py' adding 'resdk/resources/permissions.py' adding 'resdk/resources/process.py' adding 'resdk/resources/relation.py' adding 'resdk/resources/sample.py' adding 'resdk/resources/user.py' adding 'resdk/resources/utils.py' adding 'resdk/resources/kb/__init__.py' adding 'resdk/resources/kb/feature.py' adding 'resdk/resources/kb/mapping.py' adding 'resdk/shortcuts/__init__.py' adding 'resdk/shortcuts/collection.py' adding 'resdk/shortcuts/sample.py' adding 'resdk/tables/__init__.py' adding 'resdk/tables/base.py' adding 'resdk/tables/methylation.py' adding 'resdk/tables/microarray.py' adding 'resdk/tables/ml_ready.py' adding 'resdk/tables/rna.py' adding 'resdk/tables/utils.py' adding 'resdk/tables/variant.py' adding 'resdk/utils/__init__.py' adding 'resdk/utils/decorators.py' adding 'resdk/utils/table_cache.py' adding 'resdk-21.2.1.dist-info/LICENSE' adding 'resdk-21.2.1.dist-info/METADATA' adding 'resdk-21.2.1.dist-info/WHEEL' adding 'resdk-21.2.1.dist-info/top_level.txt' adding 'resdk-21.2.1.dist-info/RECORD' removing build/bdist.freebsd-14.1-STABLE-amd64/wheel Successfully built resdk-21.2.1-py3-none-any.whl =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-resdk-21.2.1 depends on package: py311-aiohttp>=3.9.3 - not found ===> Installing existing package /packages/All/py311-aiohttp-3.11.7_1.pkg [ghostbsd-14-ghostbsd_ports-job-24] Installing py311-aiohttp-3.11.7_1... [ghostbsd-14-ghostbsd_ports-job-24] `-- Installing py311-aiohappyeyeballs-2.4.3... [ghostbsd-14-ghostbsd_ports-job-24] `-- Extracting py311-aiohappyeyeballs-2.4.3: .......... done [ghostbsd-14-ghostbsd_ports-job-24] `-- Installing py311-aiosignal-1.3.1... [ghostbsd-14-ghostbsd_ports-job-24] | `-- Installing py311-frozenlist-1.5.0... [ghostbsd-14-ghostbsd_ports-job-24] | `-- Extracting py311-frozenlist-1.5.0: .......... done [ghostbsd-14-ghostbsd_ports-job-24] `-- Extracting py311-aiosignal-1.3.1: .......... done [ghostbsd-14-ghostbsd_ports-job-24] `-- Installing py311-attrs-24.2.0... [ghostbsd-14-ghostbsd_ports-job-24] `-- Extracting py311-attrs-24.2.0: .......... done [ghostbsd-14-ghostbsd_ports-job-24] `-- Installing py311-multidict-6.1.0... [ghostbsd-14-ghostbsd_ports-job-24] `-- Extracting py311-multidict-6.1.0: .......... done [ghostbsd-14-ghostbsd_ports-job-24] `-- Installing py311-propcache-0.2.0... [ghostbsd-14-ghostbsd_ports-job-24] `-- Extracting py311-propcache-0.2.0: .......... done [ghostbsd-14-ghostbsd_ports-job-24] `-- Installing py311-yarl-1.18.0_1... [ghostbsd-14-ghostbsd_ports-job-24] | `-- Installing py311-idna-3.10... [ghostbsd-14-ghostbsd_ports-job-24] | `-- Extracting py311-idna-3.10: .......... done [ghostbsd-14-ghostbsd_ports-job-24] `-- Extracting py311-yarl-1.18.0_1: .......... done [ghostbsd-14-ghostbsd_ports-job-24] Extracting py311-aiohttp-3.11.7_1: .......... done ===> py311-resdk-21.2.1 depends on package: py311-aiohttp>=3.9.3 - found ===> Returning to build of py311-resdk-21.2.1 ===> py311-resdk-21.2.1 depends on package: py311-boto3>0 - not found ===> Installing existing package /packages/All/py311-boto3-1.35.66.pkg [ghostbsd-14-ghostbsd_ports-job-24] Installing py311-boto3-1.35.66... [ghostbsd-14-ghostbsd_ports-job-24] `-- Installing py311-botocore-1.35.66... [ghostbsd-14-ghostbsd_ports-job-24] | `-- Installing py311-jmespath-1.0.1_1... [ghostbsd-14-ghostbsd_ports-job-24] | `-- Extracting py311-jmespath-1.0.1_1: .......... done [ghostbsd-14-ghostbsd_ports-job-24] | `-- Installing py311-python-dateutil-2.9.0... [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Installing py311-six-1.16.0_1... [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Extracting py311-six-1.16.0_1: .......... done [ghostbsd-14-ghostbsd_ports-job-24] | `-- Extracting py311-python-dateutil-2.9.0: .......... done [ghostbsd-14-ghostbsd_ports-job-24] | `-- Installing py311-urllib3-1.26.20,1... [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Installing py311-pysocks-1.7.1_1... [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Extracting py311-pysocks-1.7.1_1: .......... done [ghostbsd-14-ghostbsd_ports-job-24] | `-- Extracting py311-urllib3-1.26.20,1: .......... done [ghostbsd-14-ghostbsd_ports-job-24] `-- Extracting py311-botocore-1.35.66: .......... done [ghostbsd-14-ghostbsd_ports-job-24] `-- Installing py311-s3transfer-0.10.4... [ghostbsd-14-ghostbsd_ports-job-24] `-- Extracting py311-s3transfer-0.10.4: .......... done [ghostbsd-14-ghostbsd_ports-job-24] Extracting py311-boto3-1.35.66: .......... done ===== Message from py311-urllib3-1.26.20,1: -- Since version 1.25 HTTPS connections are now verified by default which is done via "cert_reqs = 'CERT_REQUIRED'". While certificate verification can be disabled via "cert_reqs = 'CERT_NONE'", it's highly recommended to leave it on. Various consumers of net/py-urllib3 already have implemented routines that either explicitly enable or disable HTTPS certificate verification (e.g. via configuration settings, CLI arguments, etc.). Yet it may happen that there are still some consumers which don't explicitly enable/disable certificate verification for HTTPS connections which could then lead to errors (as is often the case with self-signed certificates). In case of an error one should try first to temporarily disable certificate verification of the problematic urllib3 consumer to see if that approach will remedy the issue. ===> py311-resdk-21.2.1 depends on package: py311-boto3>0 - found ===> Returning to build of py311-resdk-21.2.1 ===> py311-resdk-21.2.1 depends on package: py311-botocore-stubs>0 - not found ===> Installing existing package /packages/All/py311-botocore-stubs-1.27.22.pkg [ghostbsd-14-ghostbsd_ports-job-24] Installing py311-botocore-stubs-1.27.22... [ghostbsd-14-ghostbsd_ports-job-24] Extracting py311-botocore-stubs-1.27.22: .......... done ===> py311-resdk-21.2.1 depends on package: py311-botocore-stubs>0 - found ===> Returning to build of py311-resdk-21.2.1 ===> py311-resdk-21.2.1 depends on package: py311-chardet<=5.2.0,1 - not found ===> Installing existing package /packages/All/py311-chardet-5.2.0,1.pkg [ghostbsd-14-ghostbsd_ports-job-24] Installing py311-chardet-5.2.0,1... [ghostbsd-14-ghostbsd_ports-job-24] Extracting py311-chardet-5.2.0,1: .......... done ===> py311-resdk-21.2.1 depends on package: py311-chardet<=5.2.0,1 - found ===> Returning to build of py311-resdk-21.2.1 ===> py311-resdk-21.2.1 depends on package: py311-openpyxl>0 - not found ===> Installing existing package /packages/All/py311-openpyxl-3.1.1.pkg [ghostbsd-14-ghostbsd_ports-job-24] Installing py311-openpyxl-3.1.1... [ghostbsd-14-ghostbsd_ports-job-24] `-- Installing py311-et_xmlfile-1.1.0... [ghostbsd-14-ghostbsd_ports-job-24] `-- Extracting py311-et_xmlfile-1.1.0: .......... done [ghostbsd-14-ghostbsd_ports-job-24] Extracting py311-openpyxl-3.1.1: .......... done ===> py311-resdk-21.2.1 depends on package: py311-openpyxl>0 - found ===> Returning to build of py311-resdk-21.2.1 ===> py311-resdk-21.2.1 depends on package: py311-packaging>0 - found ===> py311-resdk-21.2.1 depends on package: py311-pandas>0 - not found ===> Installing existing package /packages/All/py311-pandas-2.1.4,1.pkg [ghostbsd-14-ghostbsd_ports-job-24] Installing py311-pandas-2.1.4,1... [ghostbsd-14-ghostbsd_ports-job-24] `-- Installing py311-bottleneck-1.3.8_1... [ghostbsd-14-ghostbsd_ports-job-24] | `-- Installing py311-numpy-1.26.4_2,1... [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Installing gcc13-13.3.0... [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Installing binutils-2.43.1,1... [ghostbsd-14-ghostbsd_ports-job-24] | | | `-- Installing zstd-1.5.6... [ghostbsd-14-ghostbsd_ports-job-24] | | | `-- Installing liblz4-1.10.0,1... [ghostbsd-14-ghostbsd_ports-job-24] | | | `-- Extracting liblz4-1.10.0,1: .......... done [ghostbsd-14-ghostbsd_ports-job-24] | | | `-- Extracting zstd-1.5.6: .......... done [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Extracting binutils-2.43.1,1: .......... done [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Installing gmp-6.3.0... [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Extracting gmp-6.3.0: .......... done [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Installing mpc-1.3.1_1... [ghostbsd-14-ghostbsd_ports-job-24] | | | `-- Installing mpfr-4.2.1,1... [ghostbsd-14-ghostbsd_ports-job-24] | | | `-- Extracting mpfr-4.2.1,1: .......... done [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Extracting mpc-1.3.1_1: ......... done [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Extracting gcc13-13.3.0: .......... done [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Installing openblas-0.3.27,2... [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Extracting openblas-0.3.27,2: .......... done [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Installing suitesparse-umfpack-6.3.3_1... [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Installing suitesparse-amd-3.3.2... [ghostbsd-14-ghostbsd_ports-job-24] | | | `-- Installing suitesparse-config-7.7.0_1... [ghostbsd-14-ghostbsd_ports-job-24] | | | `-- Extracting suitesparse-config-7.7.0_1: .......... done [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Extracting suitesparse-amd-3.3.2: .......... done [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Installing suitesparse-camd-3.3.2... [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Extracting suitesparse-camd-3.3.2: .......... done [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Installing suitesparse-ccolamd-3.3.3... [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Extracting suitesparse-ccolamd-3.3.3: .......... done [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Installing suitesparse-cholmod-5.2.1_1... [ghostbsd-14-ghostbsd_ports-job-24] | | | `-- Installing suitesparse-colamd-3.3.3... [ghostbsd-14-ghostbsd_ports-job-24] | | | `-- Extracting suitesparse-colamd-3.3.3: .......... done [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Extracting suitesparse-cholmod-5.2.1_1: .......... done [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Extracting suitesparse-umfpack-6.3.3_1: .......... done [ghostbsd-14-ghostbsd_ports-job-24] | `-- Extracting py311-numpy-1.26.4_2,1: .......... done [ghostbsd-14-ghostbsd_ports-job-24] `-- Extracting py311-bottleneck-1.3.8_1: .......... done [ghostbsd-14-ghostbsd_ports-job-24] `-- Installing py311-numexpr-2.10.1... [ghostbsd-14-ghostbsd_ports-job-24] `-- Extracting py311-numexpr-2.10.1: .......... done [ghostbsd-14-ghostbsd_ports-job-24] `-- Installing py311-pytz-2024.2,1... [ghostbsd-14-ghostbsd_ports-job-24] `-- Extracting py311-pytz-2024.2,1: .......... done [ghostbsd-14-ghostbsd_ports-job-24] `-- Installing py311-sqlite3-3.11.11_7... [ghostbsd-14-ghostbsd_ports-job-24] | `-- Installing sqlite3-3.46.1,1... [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Installing libedit-3.1.20240808,1... [ghostbsd-14-ghostbsd_ports-job-24] | | `-- Extracting libedit-3.1.20240808,1: .......... done [ghostbsd-14-ghostbsd_ports-job-24] | `-- Extracting sqlite3-3.46.1,1: .......... done [ghostbsd-14-ghostbsd_ports-job-24] `-- Extracting py311-sqlite3-3.11.11_7: ........ done [ghostbsd-14-ghostbsd_ports-job-24] `-- Installing py311-tzdata-2024.2... [ghostbsd-14-ghostbsd_ports-job-24] `-- Extracting py311-tzdata-2024.2: .......... done [ghostbsd-14-ghostbsd_ports-job-24] Extracting py311-pandas-2.1.4,1: .......... done ===== Message from gcc13-13.3.0: -- 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 py311-pandas-2.1.4,1: -- Install math/py-statsmodels to enable parts of pandas.stats. Install devel/py-xarray to enable the to_xarray() function. ===> py311-resdk-21.2.1 depends on package: py311-pandas>0 - found ===> Returning to build of py311-resdk-21.2.1 ===> py311-resdk-21.2.1 depends on package: py311-pytz>0 - found ===> py311-resdk-21.2.1 depends on package: py311-requests>0 - not found ===> Installing existing package /packages/All/py311-requests-2.32.3.pkg [ghostbsd-14-ghostbsd_ports-job-24] Installing py311-requests-2.32.3... [ghostbsd-14-ghostbsd_ports-job-24] `-- Installing py311-certifi-2024.8.30... [ghostbsd-14-ghostbsd_ports-job-24] `-- Extracting py311-certifi-2024.8.30: .......... done [ghostbsd-14-ghostbsd_ports-job-24] `-- Installing py311-charset-normalizer-3.4.0... [ghostbsd-14-ghostbsd_ports-job-24] `-- Extracting py311-charset-normalizer-3.4.0: .......... done [ghostbsd-14-ghostbsd_ports-job-24] Extracting py311-requests-2.32.3: .......... done ===> py311-resdk-21.2.1 depends on package: py311-requests>0 - found ===> Returning to build of py311-resdk-21.2.1 ===> py311-resdk-21.2.1 depends on package: py311-slumber>=0.7.1 - not found ===> Installing existing package /packages/All/py311-slumber-0.7.1_1.pkg [ghostbsd-14-ghostbsd_ports-job-24] Installing py311-slumber-0.7.1_1... [ghostbsd-14-ghostbsd_ports-job-24] Extracting py311-slumber-0.7.1_1: .......... done ===> py311-resdk-21.2.1 depends on package: py311-slumber>=0.7.1 - found ===> Returning to build of py311-resdk-21.2.1 ===> py311-resdk-21.2.1 depends on package: py311-tqdm>0 - not found ===> Installing existing package /packages/All/py311-tqdm-4.67.0.pkg [ghostbsd-14-ghostbsd_ports-job-24] Installing py311-tqdm-4.67.0... [ghostbsd-14-ghostbsd_ports-job-24] Extracting py311-tqdm-4.67.0: .......... done ===> py311-resdk-21.2.1 depends on package: py311-tqdm>0 - found ===> Returning to build of py311-resdk-21.2.1 ===> py311-resdk-21.2.1 depends on package: py311-tzlocal>0 - not found ===> Installing existing package /packages/All/py311-tzlocal-5.2.pkg [ghostbsd-14-ghostbsd_ports-job-24] Installing py311-tzlocal-5.2... [ghostbsd-14-ghostbsd_ports-job-24] `-- Installing py311-pytz-deprecation-shim-0.1.0.post0_3... [ghostbsd-14-ghostbsd_ports-job-24] `-- Extracting py311-pytz-deprecation-shim-0.1.0.post0_3: .......... done [ghostbsd-14-ghostbsd_ports-job-24] Extracting py311-tzlocal-5.2: .......... done ===> py311-resdk-21.2.1 depends on package: py311-tzlocal>0 - found ===> Returning to build of py311-resdk-21.2.1 ===> py311-resdk-21.2.1 depends on package: py311-wrapt>0 - not found ===> Installing existing package /packages/All/py311-wrapt-1.16.0_1.pkg [ghostbsd-14-ghostbsd_ports-job-24] Installing py311-wrapt-1.16.0_1... [ghostbsd-14-ghostbsd_ports-job-24] Extracting py311-wrapt-1.16.0_1: .......... done ===> py311-resdk-21.2.1 depends on package: py311-wrapt>0 - found ===> Returning to build of py311-resdk-21.2.1 ===> py311-resdk-21.2.1 depends on package: py311-xlrd>0 - not found ===> Installing existing package /packages/All/py311-xlrd-2.0.1_1.pkg [ghostbsd-14-ghostbsd_ports-job-24] Installing py311-xlrd-2.0.1_1... [ghostbsd-14-ghostbsd_ports-job-24] Extracting py311-xlrd-2.0.1_1: .......... done ===> py311-resdk-21.2.1 depends on package: py311-xlrd>0 - found ===> Returning to build of py311-resdk-21.2.1 ===> py311-resdk-21.2.1 depends on package: py311-mypy-boto3-s3>0 - not found ===> Installing existing package /packages/All/py311-mypy-boto3-s3-1.34.120.pkg [ghostbsd-14-ghostbsd_ports-job-24] Installing py311-mypy-boto3-s3-1.34.120... [ghostbsd-14-ghostbsd_ports-job-24] Extracting py311-mypy-boto3-s3-1.34.120: .......... done ===> py311-resdk-21.2.1 depends on package: py311-mypy-boto3-s3>0 - found ===> Returning to build of py311-resdk-21.2.1 ===> py311-resdk-21.2.1 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Staging for py311-resdk-21.2.1 ===> 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=2024-12-14T19:13:30+0000' 'PKG_NOTE_ports_top_git_hash=b4bf4e75f8c6' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=335c5d9d8a83' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.1_1' NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building packages for py311-resdk-21.2.1 ===> Building py311-resdk-21.2.1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py311-resdk-21.2.1 build of biology/py-resdk@py311 | py311-resdk-21.2.1 ended at Sat Dec 14 14:17:40 EST 2024 build time: 00:04:17