Started by upstream project "Trigger" build number 126 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 2.39.3' > 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 b471efda0cc72dadb3a1baf21fb23f861f74ad94 (refs/remotes/origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f b471efda0cc72dadb3a1baf21fb23f861f74ad94 # timeout=10 Commit message: "Merge pull request #611 from melissalinkert/columbus-position-units" > git rev-list --no-walk b471efda0cc72dadb3a1baf21fb23f861f74ad94 # timeout=10 [merge-ci] $ /bin/bash -xe /tmp/jenkins5428116393425627008.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 (24.1.1) + /tmp/venv/bin/pip install -U scc Requirement already satisfied: scc in /tmp/venv/lib/python3.9/site-packages (0.20.0) Requirement already satisfied: PyGithub>=1.54 in /tmp/venv/lib/python3.9/site-packages (from scc) (2.3.0) Requirement already satisfied: PyYAML>=5.1 in /tmp/venv/lib/python3.9/site-packages (from scc) (6.0.1) Requirement already satisfied: future in /tmp/venv/lib/python3.9/site-packages (from scc) (1.0.0) Requirement already satisfied: ruamel.yaml in /tmp/venv/lib/python3.9/site-packages (from scc) (0.18.6) Requirement already satisfied: ruamel.yaml.jinja2 in /tmp/venv/lib/python3.9/site-packages (from scc) (0.2.7) Requirement already satisfied: six in /tmp/venv/lib/python3.9/site-packages (from scc) (1.16.0) Requirement already satisfied: urllib3<2 in /tmp/venv/lib/python3.9/site-packages (from scc) (1.26.18) Requirement already satisfied: yaclifw<0.3,>=0.2.0 in /tmp/venv/lib/python3.9/site-packages (from scc) (0.2.0) Requirement already satisfied: pynacl>=1.4.0 in /tmp/venv/lib/python3.9/site-packages (from PyGithub>=1.54->scc) (1.5.0) Requirement already satisfied: requests>=2.14.0 in /tmp/venv/lib/python3.9/site-packages (from PyGithub>=1.54->scc) (2.31.0) Requirement already satisfied: pyjwt>=2.4.0 in /tmp/venv/lib/python3.9/site-packages (from pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) (2.8.0) Requirement already satisfied: typing-extensions>=4.0.0 in /tmp/venv/lib/python3.9/site-packages (from PyGithub>=1.54->scc) (4.11.0) Requirement already satisfied: Deprecated in /tmp/venv/lib/python3.9/site-packages (from PyGithub>=1.54->scc) (1.2.14) Requirement already satisfied: ruamel.yaml.clib>=0.2.7 in /tmp/venv/lib/python3.9/site-packages (from ruamel.yaml->scc) (0.2.8) Requirement already satisfied: cryptography>=3.4.0 in /tmp/venv/lib/python3.9/site-packages (from pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) (42.0.5) Requirement already satisfied: cffi>=1.4.1 in /tmp/venv/lib/python3.9/site-packages (from pynacl>=1.4.0->PyGithub>=1.54->scc) (1.16.0) Requirement already satisfied: charset-normalizer<4,>=2 in /tmp/venv/lib/python3.9/site-packages (from requests>=2.14.0->PyGithub>=1.54->scc) (3.3.2) Requirement already satisfied: idna<4,>=2.5 in /tmp/venv/lib/python3.9/site-packages (from requests>=2.14.0->PyGithub>=1.54->scc) (3.7) Requirement already satisfied: certifi>=2017.4.17 in /tmp/venv/lib/python3.9/site-packages (from requests>=2.14.0->PyGithub>=1.54->scc) (2024.2.2) Requirement already satisfied: wrapt<2,>=1.10 in /tmp/venv/lib/python3.9/site-packages (from Deprecated->PyGithub>=1.54->scc) (1.16.0) Requirement already satisfied: pycparser in /tmp/venv/lib/python3.9/site-packages (from cffi>=1.4.1->pynacl>=1.4.0->PyGithub>=1.54->scc) (2.22) + test -e src + /tmp/venv/bin/scc merge master --no-ask --reset --comment --push merge_ci 2024-07-06 00:00:29,215 [ scc.merge] INFO Merging Pull Request(s) based on master 2024-07-06 00:00:29,215 [ scc.merge] INFO Including Pull Request(s) opened by any public member of the organization 2024-07-06 00:00:29,215 [ scc.merge] INFO Including Pull Request(s) labelled as include or dependencies 2024-07-06 00:00:29,215 [ scc.merge] INFO Excluding Pull Request(s) staged as draft 2024-07-06 00:00:29,215 [ scc.merge] INFO Excluding Pull Request(s) labelled as exclude or breaking 2024-07-06 00:00:49,490 [ scc.merge] INFO Repository: openmicroscopy/data_repo_config 2024-07-06 00:00:49,490 [ scc.merge] INFO Excluded PRs: 2024-07-06 00:00:49,490 [ scc.merge] INFO - PR 546 melissalinkert 'InCell updates' (label: exclude) 2024-07-06 00:00:49,490 [ scc.merge] INFO Already up to date. 2024-07-06 00:00:49,490 [ scc.merge] INFO 2024-07-06 00:00:49,490 [ scc.merge] INFO Merged PRs: 2024-07-06 00:00:49,491 [ scc.merge] INFO - PR 610 melissalinkert 'Add dataset from https://github.com/ome/bioformats/issues/4165' 2024-07-06 00:00:49,491 [ scc.merge] INFO - PR 612 melissalinkert 'DICOM: swap Z and T for datasets newly detected as timelapse' 2024-07-06 00:00:49,491 [ scc.merge] INFO - PR 613 melissalinkert 'Add dataset for https://github.com/ome/bioformats/pull/4197' 2024-07-06 00:00:49,491 [ scc.merge] INFO - PR 614 melissalinkert 'Add dataset for https://github.com/ome/bioformats/pull/4198' 2024-07-06 00:00:49,491 [ scc.merge] INFO - PR 615 melissalinkert 'Add CV7000 example where TIFFs are in a subdirectory' 2024-07-06 00:00:49,491 [ scc.merge] INFO - PR 616 sbesson 'Add configuration file for idr0043 sample file' 2024-07-06 00:00:49,491 [ scc.merge] INFO 2024-07-06 00:00:51,995 [ scc.merge] INFO Merged branch pushed to https://github.com/snoopycrimecop/data_repo_config/tree/merge_ci Finished: SUCCESS