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Started by upstream project "Trigger" build number 515 originally caused by: Started by timer Running as SYSTEM Building remotely on testintegration (swarm rocky9 ice36 java11) in workspace /uod/idr-scratch/merge-ci The recommended git tool is: NONE No credentials specified > git rev-parse --resolve-git-dir /uod/idr-scratch/merge-ci/.git # timeout=10 Fetching changes from the remote Git repository > git config remote.origin.url git@github.com:openmicroscopy/data_repo_config.git # timeout=10 Fetching upstream changes from git@github.com:openmicroscopy/data_repo_config.git > git --version # timeout=10 > git --version # 'git version 2.43.5' > git fetch --tags --force --progress -- git@github.com:openmicroscopy/data_repo_config.git +refs/heads/*:refs/remotes/origin/* # timeout=10 > git rev-parse refs/remotes/origin/master^{commit} # timeout=10 Checking out Revision c830e220bb207640a2b6aac312c5478b3c85e45a (refs/remotes/origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f c830e220bb207640a2b6aac312c5478b3c85e45a # timeout=10 Commit message: "Merge pull request #652 from melissalinkert/gh-4309" > git rev-list --no-walk c830e220bb207640a2b6aac312c5478b3c85e45a # timeout=10 [merge-ci] $ /bin/bash -xe /tmp/jenkins18408665740401307945.sh + python3 -mvenv /tmp/venv + source /tmp/venv/bin/activate ++ deactivate nondestructive ++ '[' -n '' ']' ++ '[' -n '' ']' ++ '[' -n /bin/bash -o -n '' ']' ++ hash -r ++ '[' -n '' ']' ++ unset VIRTUAL_ENV ++ '[' '!' nondestructive = nondestructive ']' ++ VIRTUAL_ENV=/tmp/venv ++ export VIRTUAL_ENV ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ++ PATH=/tmp/venv/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ++ export PATH ++ '[' -n '' ']' ++ '[' -z '' ']' ++ _OLD_VIRTUAL_PS1= ++ PS1='(venv) ' ++ export PS1 ++ '[' -n /bin/bash -o -n '' ']' ++ hash -r + /tmp/venv/bin/pip install -U pip Requirement already satisfied: pip in /tmp/venv/lib/python3.9/site-packages (21.3.1) Collecting pip Using cached pip-25.1.1-py3-none-any.whl (1.8 MB) Installing collected packages: pip Attempting uninstall: pip Found existing installation: pip 21.3.1 Uninstalling pip-21.3.1: Successfully uninstalled pip-21.3.1 Successfully installed pip-25.1.1 + /tmp/venv/bin/pip install -U scc Collecting scc Using cached scc-0.20.0-py3-none-any.whl.metadata (3.6 kB) Collecting PyGithub>=1.54 (from scc) Using cached PyGithub-2.6.1-py3-none-any.whl.metadata (3.9 kB) Collecting PyYAML>=5.1 (from scc) Downloading PyYAML-6.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB) Collecting future (from scc) Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB) Collecting ruamel.yaml (from scc) Using cached ruamel.yaml-0.18.14-py3-none-any.whl.metadata (24 kB) Collecting ruamel.yaml.jinja2 (from scc) Using cached ruamel.yaml.jinja2-0.2.7-py2.py3-none-any.whl.metadata (2.9 kB) Collecting six (from scc) Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB) Collecting urllib3<2 (from scc) Using cached urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB) Collecting yaclifw<0.3,>=0.2.0 (from scc) Using cached yaclifw-0.2.0.tar.gz (13 kB) Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting pynacl>=1.4.0 (from PyGithub>=1.54->scc) Using cached PyNaCl-1.5.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl.metadata (8.6 kB) Collecting requests>=2.14.0 (from PyGithub>=1.54->scc) Using cached requests-2.32.4-py3-none-any.whl.metadata (4.9 kB) Collecting pyjwt>=2.4.0 (from pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) Using cached PyJWT-2.10.1-py3-none-any.whl.metadata (4.0 kB) Collecting typing-extensions>=4.0.0 (from PyGithub>=1.54->scc) Using cached typing_extensions-4.14.0-py3-none-any.whl.metadata (3.0 kB) Collecting Deprecated (from PyGithub>=1.54->scc) Using cached Deprecated-1.2.18-py2.py3-none-any.whl.metadata (5.7 kB) Collecting cryptography>=3.4.0 (from pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) Downloading cryptography-45.0.4-cp37-abi3-manylinux_2_34_x86_64.whl.metadata (5.7 kB) Collecting cffi>=1.14 (from cryptography>=3.4.0->pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) Downloading cffi-1.17.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.5 kB) Collecting pycparser (from cffi>=1.14->cryptography>=3.4.0->pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) Using cached pycparser-2.22-py3-none-any.whl.metadata (943 bytes) Collecting charset_normalizer<4,>=2 (from requests>=2.14.0->PyGithub>=1.54->scc) Downloading charset_normalizer-3.4.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (35 kB) Collecting idna<4,>=2.5 (from requests>=2.14.0->PyGithub>=1.54->scc) Using cached idna-3.10-py3-none-any.whl.metadata (10 kB) Collecting certifi>=2017.4.17 (from requests>=2.14.0->PyGithub>=1.54->scc) Using cached certifi-2025.4.26-py3-none-any.whl.metadata (2.5 kB) Collecting wrapt<2,>=1.10 (from Deprecated->PyGithub>=1.54->scc) Downloading wrapt-1.17.2-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.4 kB) Collecting ruamel.yaml.clib>=0.2.7 (from ruamel.yaml->scc) Downloading ruamel.yaml.clib-0.2.12-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.7 kB) Using cached scc-0.20.0-py3-none-any.whl (48 kB) Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB) Using cached PyGithub-2.6.1-py3-none-any.whl (410 kB) Using cached PyJWT-2.10.1-py3-none-any.whl (22 kB) Downloading cryptography-45.0.4-cp37-abi3-manylinux_2_34_x86_64.whl (4.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.5/4.5 MB 22.8 MB/s eta 0:00:00 Downloading cffi-1.17.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (445 kB) Using cached PyNaCl-1.5.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (856 kB) Downloading PyYAML-6.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (737 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 737.4/737.4 kB 26.7 MB/s eta 0:00:00 Using cached requests-2.32.4-py3-none-any.whl (64 kB) Downloading charset_normalizer-3.4.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (149 kB) Using cached idna-3.10-py3-none-any.whl (70 kB) Using cached certifi-2025.4.26-py3-none-any.whl (159 kB) Using cached typing_extensions-4.14.0-py3-none-any.whl (43 kB) Using cached Deprecated-1.2.18-py2.py3-none-any.whl (10.0 kB) Downloading wrapt-1.17.2-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (82 kB) Using cached future-1.0.0-py3-none-any.whl (491 kB) Using cached pycparser-2.22-py3-none-any.whl (117 kB) Using cached ruamel.yaml-0.18.14-py3-none-any.whl (118 kB) Downloading ruamel.yaml.clib-0.2.12-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (724 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 724.9/724.9 kB 26.7 MB/s eta 0:00:00 Using cached ruamel.yaml.jinja2-0.2.7-py2.py3-none-any.whl (5.5 kB) Using cached six-1.17.0-py2.py3-none-any.whl (11 kB) Building wheels for collected packages: yaclifw Building wheel for yaclifw (pyproject.toml): started Building wheel for yaclifw (pyproject.toml): finished with status 'done' Created wheel for yaclifw: filename=yaclifw-0.2.0-py3-none-any.whl size=14689 sha256=dabf3eb5d801fb38bd5b6aede95099536143385ffbed1351821ca381b5a9dbe9 Stored in directory: /home/omero/.cache/pip/wheels/ef/84/32/3fc0bc762a5cc68989b94674f5a9b9f0730cc5c4bef0bfe154 Successfully built yaclifw Installing collected packages: wrapt, urllib3, typing-extensions, six, ruamel.yaml.clib, PyYAML, pyjwt, pycparser, idna, future, charset_normalizer, certifi, yaclifw, ruamel.yaml, requests, Deprecated, cffi, ruamel.yaml.jinja2, pynacl, cryptography, PyGithub, scc Successfully installed Deprecated-1.2.18 PyGithub-2.6.1 PyYAML-6.0.2 certifi-2025.4.26 cffi-1.17.1 charset_normalizer-3.4.2 cryptography-45.0.4 future-1.0.0 idna-3.10 pycparser-2.22 pyjwt-2.10.1 pynacl-1.5.0 requests-2.32.4 ruamel.yaml-0.18.14 ruamel.yaml.clib-0.2.12 ruamel.yaml.jinja2-0.2.7 scc-0.20.0 six-1.17.0 typing-extensions-4.14.0 urllib3-1.26.20 wrapt-1.17.2 yaclifw-0.2.0 + test -e src + /tmp/venv/bin/scc merge master --no-ask --reset --comment --push merge_ci 2025-06-12 00:00:55,865 [ scc.merge] INFO Merging Pull Request(s) based on master 2025-06-12 00:00:55,865 [ scc.merge] INFO Including Pull Request(s) opened by any public member of the organization 2025-06-12 00:00:55,865 [ scc.merge] INFO Including Pull Request(s) labelled as include or dependencies 2025-06-12 00:00:55,865 [ scc.merge] INFO Excluding Pull Request(s) staged as draft 2025-06-12 00:00:55,865 [ scc.merge] INFO Excluding Pull Request(s) labelled as exclude or breaking 2025-06-12 00:01:57,020 [ scc.merge] INFO Repository: openmicroscopy/data_repo_config 2025-06-12 00:01:57,021 [ scc.merge] INFO Excluded PRs: 2025-06-12 00:01:57,021 [ scc.merge] INFO - PR 612 melissalinkert 'DICOM: swap Z and T for datasets newly detected as timelapse' (label: exclude) 2025-06-12 00:01:57,021 [ scc.merge] INFO - PR 546 melissalinkert 'InCell updates' (label: exclude) 2025-06-12 00:01:57,021 [ scc.merge] INFO Already up to date. 2025-06-12 00:01:57,021 [ scc.merge] INFO 2025-06-12 00:01:57,021 [ scc.merge] INFO Merged PRs: 2025-06-12 00:01:57,021 [ scc.merge] INFO - PR 655 melissalinkert 'Add example companion dataset with one Image that has no linked data' 2025-06-12 00:01:57,021 [ scc.merge] INFO - PR 656 sbesson 'Additional ND2 samples for Bio-Formats 8.3.0' 2025-06-12 00:01:57,021 [ scc.merge] INFO - PR 657 melissalinkert 'Add datasets for https://github.com/ome/bioformats/issues/3761' 2025-06-12 00:01:57,021 [ scc.merge] INFO - PR 658 melissalinkert 'Metamorph HCS updates' 2025-06-12 00:01:57,021 [ scc.merge] INFO - PR 659 melissalinkert 'Add Modulo configuration for LI-FLIM data' 2025-06-12 00:01:57,021 [ scc.merge] INFO - PR 660 melissalinkert 'Add remaining Modulo configuration' 2025-06-12 00:01:57,021 [ scc.merge] INFO 2025-06-12 00:02:00,188 [ scc.merge] INFO Merged branch pushed to https://github.com/snoopycrimecop/data_repo_config/tree/merge_ci Finished: SUCCESS