Started by upstream project "Trigger" build number 1 originally caused by: Started by user devspace Running as SYSTEM Building remotely on testintegration (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/BIOFORMATS-push The recommended git tool is: NONE No credentials specified Cloning the remote Git repository Cloning repository https://github.com/ome/bio-formats-build > git init /home/omero/workspace/BIOFORMATS-push/bio-formats-build # timeout=10 Fetching upstream changes from https://github.com/ome/bio-formats-build > git --version # timeout=10 > git --version # 'git version 2.39.3' > git fetch --tags --force --progress -- https://github.com/ome/bio-formats-build +refs/heads/*:refs/remotes/origin/* # timeout=10 > git config remote.origin.url https://github.com/ome/bio-formats-build # timeout=10 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10 Avoid second fetch > git rev-parse origin/master^{commit} # timeout=10 Checking out Revision e7ea0c022f87bdf67c4090bdcd8c10c2f2014607 (origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f e7ea0c022f87bdf67c4090bdcd8c10c2f2014607 # timeout=10 Commit message: "Merge pull request #568 from ome/dependabot/submodules/bio-formats-documentation-817d09e" First time build. Skipping changelog. > git remote # timeout=10 > git submodule init # timeout=10 > git submodule sync # timeout=10 > git config --get remote.origin.url # timeout=10 > git submodule init # timeout=10 > git config -f .gitmodules --get-regexp ^submodule\.(.+)\.url # timeout=10 > git config --get submodule.ome-common-java.url # timeout=10 > git config -f .gitmodules --get submodule.ome-common-java.path # timeout=10 > git config --get submodule.ome-model.url # timeout=10 > git config -f .gitmodules --get submodule.ome-model.path # timeout=10 > git config --get submodule.ome-poi.url # timeout=10 > git config -f .gitmodules --get submodule.ome-poi.path # timeout=10 > git config --get submodule.ome-mdbtools.url # timeout=10 > git config -f .gitmodules --get submodule.ome-mdbtools.path # timeout=10 > git config --get submodule.ome-jai.url # timeout=10 > git config -f .gitmodules --get submodule.ome-jai.path # timeout=10 > git config --get submodule.ome-codecs.url # timeout=10 > git config -f .gitmodules --get submodule.ome-codecs.path # timeout=10 > git config --get submodule.ome-metakit.url # timeout=10 > git config -f .gitmodules --get submodule.ome-metakit.path # timeout=10 > git config --get submodule.ome-stubs.url # timeout=10 > git config -f .gitmodules --get submodule.ome-stubs.path # timeout=10 > git config --get submodule.bioformats.url # timeout=10 > git config -f .gitmodules --get submodule.bioformats.path # timeout=10 > git config --get submodule.bio-formats-documentation.url # timeout=10 > git config -f .gitmodules --get submodule.bio-formats-documentation.path # timeout=10 > git config --get submodule.bio-formats-examples.url # timeout=10 > git config -f .gitmodules --get submodule.bio-formats-examples.path # timeout=10 > git config --get submodule.ZarrReader.url # timeout=10 > git config -f .gitmodules --get submodule.ZarrReader.path # timeout=10 > git submodule update --init --recursive --remote ome-common-java # timeout=10 > git submodule update --init --recursive --remote ome-model # timeout=10 > git submodule update --init --recursive --remote ome-poi # timeout=10 > git submodule update --init --recursive --remote ome-mdbtools # timeout=10 > git submodule update --init --recursive --remote ome-jai # timeout=10 > git submodule update --init --recursive --remote ome-codecs # timeout=10 > git submodule update --init --recursive --remote ome-metakit # timeout=10 > git submodule update --init --recursive --remote ome-stubs # timeout=10 > git submodule update --init --recursive --remote bioformats # timeout=10 > git submodule update --init --recursive --remote bio-formats-documentation # timeout=10 > git submodule update --init --recursive --remote bio-formats-examples # timeout=10 > git submodule update --init --recursive --remote ZarrReader # timeout=10 [BIOFORMATS-push] $ /bin/bash -xe /tmp/jenkins6232610743317721656.sh + python3 -mvenv venv + source /home/omero/workspace/BIOFORMATS-push/venv/bin/activate ++ deactivate nondestructive ++ '[' -n '' ']' ++ '[' -n '' ']' ++ '[' -n /bin/bash -o -n '' ']' ++ hash -r ++ '[' -n '' ']' ++ unset VIRTUAL_ENV ++ '[' '!' nondestructive = nondestructive ']' ++ VIRTUAL_ENV=/home/omero/workspace/BIOFORMATS-push/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=/home/omero/workspace/BIOFORMATS-push/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 + pip install -U pip Requirement already satisfied: pip in ./venv/lib/python3.9/site-packages (21.2.3) Collecting pip Using cached pip-24.0-py3-none-any.whl (2.1 MB) Installing collected packages: pip Attempting uninstall: pip Found existing installation: pip 21.2.3 Uninstalling pip-21.2.3: Successfully uninstalled pip-21.2.3 Successfully installed pip-24.0 + pip install -U scc Collecting scc Using cached scc-0.19.1-py3-none-any.whl.metadata (3.6 kB) Collecting PyGithub>=1.54 (from scc) Using cached PyGithub-2.2.0-py3-none-any.whl.metadata (3.8 kB) Collecting PyYAML>=5.1 (from scc) Using cached PyYAML-6.0.1-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-0.18.6-py3-none-any.whl.metadata (23 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-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB) Collecting urllib3<2 (from scc) Using cached urllib3-1.26.18-py2.py3-none-any.whl.metadata (48 kB) Collecting yaclifw<0.3,>=0.2.0 (from scc) Using cached yaclifw-0.2.0-py3-none-any.whl 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-2.31.0-py3-none-any.whl.metadata (4.6 kB) Collecting pyjwt>=2.4.0 (from pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) Using cached PyJWT-2.8.0-py3-none-any.whl.metadata (4.2 kB) Collecting typing-extensions>=4.0.0 (from PyGithub>=1.54->scc) Using cached typing_extensions-4.10.0-py3-none-any.whl.metadata (3.0 kB) Collecting Deprecated (from PyGithub>=1.54->scc) Using cached Deprecated-1.2.14-py2.py3-none-any.whl.metadata (5.4 kB) Collecting ruamel.yaml.clib>=0.2.7 (from ruamel.yaml->scc) Using cached ruamel.yaml.clib-0.2.8-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl.metadata (2.2 kB) Collecting cryptography>=3.4.0 (from pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) Using cached cryptography-42.0.5-cp39-abi3-manylinux_2_28_x86_64.whl.metadata (5.3 kB) Collecting cffi>=1.4.1 (from pynacl>=1.4.0->PyGithub>=1.54->scc) Using cached cffi-1.16.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.5 kB) Collecting charset-normalizer<4,>=2 (from requests>=2.14.0->PyGithub>=1.54->scc) Using cached charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB) Collecting idna<4,>=2.5 (from requests>=2.14.0->PyGithub>=1.54->scc) Using cached idna-3.6-py3-none-any.whl.metadata (9.9 kB) Collecting certifi>=2017.4.17 (from requests>=2.14.0->PyGithub>=1.54->scc) Using cached certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB) Collecting wrapt<2,>=1.10 (from Deprecated->PyGithub>=1.54->scc) Using cached wrapt-1.16.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.6 kB) Collecting pycparser (from cffi>=1.4.1->pynacl>=1.4.0->PyGithub>=1.54->scc) Using cached pycparser-2.21-py2.py3-none-any.whl.metadata (1.1 kB) Using cached scc-0.19.1-py3-none-any.whl (48 kB) Using cached PyGithub-2.2.0-py3-none-any.whl (350 kB) Using cached PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (738 kB) Using cached urllib3-1.26.18-py2.py3-none-any.whl (143 kB) Using cached future-1.0.0-py3-none-any.whl (491 kB) Using cached ruamel.yaml-0.18.6-py3-none-any.whl (117 kB) Using cached ruamel.yaml.jinja2-0.2.7-py2.py3-none-any.whl (5.5 kB) Using cached six-1.16.0-py2.py3-none-any.whl (11 kB) Using cached PyJWT-2.8.0-py3-none-any.whl (22 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) Using cached requests-2.31.0-py3-none-any.whl (62 kB) Using cached ruamel.yaml.clib-0.2.8-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl (562 kB) Using cached typing_extensions-4.10.0-py3-none-any.whl (33 kB) Using cached Deprecated-1.2.14-py2.py3-none-any.whl (9.6 kB) Using cached certifi-2024.2.2-py3-none-any.whl (163 kB) Using cached cffi-1.16.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (443 kB) Using cached charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (142 kB) Using cached cryptography-42.0.5-cp39-abi3-manylinux_2_28_x86_64.whl (4.6 MB) Using cached idna-3.6-py3-none-any.whl (61 kB) Using cached wrapt-1.16.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (80 kB) Using cached pycparser-2.21-py2.py3-none-any.whl (118 kB) 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-1.2.14 PyGithub-2.2.0 PyYAML-6.0.1 certifi-2024.2.2 cffi-1.16.0 charset-normalizer-3.3.2 cryptography-42.0.5 future-1.0.0 idna-3.6 pycparser-2.21 pyjwt-2.8.0 pynacl-1.5.0 requests-2.31.0 ruamel.yaml-0.18.6 ruamel.yaml.clib-0.2.8 ruamel.yaml.jinja2-0.2.7 scc-0.19.1 six-1.16.0 typing-extensions-4.10.0 urllib3-1.26.18 wrapt-1.16.0 yaclifw-0.2.0 + PATH=/home/omero/workspace/BIOFORMATS-push/bio-formats-build/scripts:/home/omero/workspace/BIOFORMATS-push/venv/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin + MERGE_OPTIONS='--no-ask --reset --comment -S success-only' + cd bio-formats-build + echo 'Merge base repository (no submodule updates)' Merge base repository (no submodule updates) + scc merge --no-ask --reset --comment -S success-only --shallow master 2024-03-14 15:38:16,392 [ scc.merge] INFO Merging Pull Request(s) based on master 2024-03-14 15:38:16,392 [ scc.merge] INFO Including Pull Request(s) opened by any public member of the organization 2024-03-14 15:38:16,392 [ scc.merge] INFO Including Pull Request(s) labelled as include or dependencies 2024-03-14 15:38:16,392 [ scc.merge] INFO Excluding Pull Request(s) staged as draft 2024-03-14 15:38:16,392 [ scc.merge] INFO Excluding Pull Request(s) labelled as exclude or breaking 2024-03-14 15:38:16,392 [ scc.merge] INFO Excluding Pull Request(s) without successful status 2024-03-14 15:38:35,320 [ scc.merge] INFO Repository: ome/bio-formats-build 2024-03-14 15:38:35,320 [ scc.merge] INFO Already up to date. 2024-03-14 15:38:35,320 [ scc.merge] INFO 2024-03-14 15:38:35,320 [ scc.merge] INFO Merged PRs: 2024-03-14 15:38:35,320 [ scc.merge] INFO - PR 567 dependabot[bot] 'Bump ZarrReader from `4deea8d` to `cf4f3f2`' 2024-03-14 15:38:35,320 [ scc.merge] INFO - PR 570 dependabot[bot] 'Bump ome-common-java from `fa81e2b` to `eca9c1c`' 2024-03-14 15:38:35,320 [ scc.merge] INFO - PR 571 dependabot[bot] 'Bump bioformats from `6815841` to `83df5ca`' 2024-03-14 15:38:35,320 [ scc.merge] INFO - PR 572 dependabot[bot] 'Bump ome-poi from `ba0d5d2` to `1fcfd18`' 2024-03-14 15:38:35,320 [ scc.merge] INFO - PR 573 dependabot[bot] 'Bump ome-codecs from `040c8b9` to `e092dea`' 2024-03-14 15:38:35,320 [ scc.merge] INFO + git submodule sync Synchronizing submodule url for 'ZarrReader' Synchronizing submodule url for 'bio-formats-documentation' Synchronizing submodule url for 'bio-formats-examples' Synchronizing submodule url for 'bioformats' Synchronizing submodule url for 'ome-codecs' Synchronizing submodule url for 'ome-common-java' Synchronizing submodule url for 'ome-jai' Synchronizing submodule url for 'ome-mdbtools' Synchronizing submodule url for 'ome-metakit' Synchronizing submodule url for 'ome-model' Synchronizing submodule url for 'ome-poi' Synchronizing submodule url for 'ome-stubs' + git submodule update --remote --recursive Submodule path 'ome-metakit': checked out '21bd75668a005effa65cb89404623d056fcee9b2' + echo 'Merge all submodules using repository configuration:' Merge all submodules using repository configuration: + cat scripts/repositories.yml base-branch: master submodules: ome-common-java: base-branch: master bioformats: base-branch: develop bio-formats-documentation: base-branch: master bio-formats-examples: base-branch: master ome-codecs: base-branch: master ome-common-java: base-branch: master ome-jai: base-branch: master ome-mdbtools: base-branch: master ome-metakit: base-branch: master ome-model: base-branch: master ome-poi: base-branch: master ome-stubs: base-branch: master ZarrReader: base-branch: main ++ pwd + scc merge --repository-config=/home/omero/workspace/BIOFORMATS-push/bio-formats-build/scripts/repositories.yml --no-ask --reset --comment -S success-only --update-gitmodules --push merge_ci master Following Github server redirection from /repos/openmicroscopy/bioformats to /repositories/2510503 2024-03-14 15:38:50,822 [github.Reque] INFO Following Github server redirection from /repos/openmicroscopy/bioformats to /repositories/2510503 2024-03-14 15:39:10,898 [ scc.merge] INFO Merging Pull Request(s) based on master 2024-03-14 15:39:10,899 [ scc.merge] INFO Including Pull Request(s) opened by any public member of the organization 2024-03-14 15:39:10,899 [ scc.merge] INFO Including Pull Request(s) labelled as include or dependencies 2024-03-14 15:39:10,899 [ scc.merge] INFO Excluding Pull Request(s) staged as draft 2024-03-14 15:39:10,899 [ scc.merge] INFO Excluding Pull Request(s) labelled as exclude or breaking 2024-03-14 15:39:10,899 [ scc.merge] INFO Excluding Pull Request(s) without successful status 2024-03-14 15:39:29,425 [ scc.git] INFO Overriding base-branch from master to main 2024-03-14 15:40:03,253 [ scc.git] INFO Overriding base-branch from master to develop 2024-03-14 15:41:29,420 [ scc.git] INFO - PR 174 jburel 'Remove docs' Conflicting PR. Removed from build [BIOFORMATS-push#1](https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1/). See the [console output](https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1/consoleText) for more details. Possible conflicts: - Upstream changes - docs/sphinx/pom.xml --conflicts 2024-03-14 15:41:44,490 [ scc.merge] INFO Repository: ome/bio-formats-build 2024-03-14 15:41:44,490 [ scc.merge] INFO Already up to date. 2024-03-14 15:41:44,490 [ scc.merge] INFO 2024-03-14 15:41:44,490 [ scc.merge] INFO Merged PRs: 2024-03-14 15:41:44,490 [ scc.merge] INFO - PR 567 dependabot[bot] 'Bump ZarrReader from `4deea8d` to `cf4f3f2`' 2024-03-14 15:41:44,490 [ scc.merge] INFO - PR 570 dependabot[bot] 'Bump ome-common-java from `fa81e2b` to `eca9c1c`' 2024-03-14 15:41:44,490 [ scc.merge] INFO - PR 571 dependabot[bot] 'Bump bioformats from `6815841` to `83df5ca`' 2024-03-14 15:41:44,490 [ scc.merge] INFO - PR 572 dependabot[bot] 'Bump ome-poi from `ba0d5d2` to `1fcfd18`' 2024-03-14 15:41:44,490 [ scc.merge] INFO - PR 573 dependabot[bot] 'Bump ome-codecs from `040c8b9` to `e092dea`' 2024-03-14 15:41:44,490 [ scc.merge] INFO 2024-03-14 15:41:44,490 [ scc.merge] INFO Repository: ome/ZarrReader 2024-03-14 15:41:44,490 [ scc.merge] INFO Excluded PRs: 2024-03-14 15:41:44,490 [ scc.merge] INFO - PR 73 dgault 'Update ReadMe and Change Log' (status: failure) 2024-03-14 15:41:44,490 [ scc.merge] INFO - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 2024-03-14 15:41:44,490 [ scc.merge] INFO Already up to date. 2024-03-14 15:41:44,490 [ scc.merge] INFO 2024-03-14 15:41:44,490 [ scc.merge] INFO Merged PRs: 2024-03-14 15:41:44,490 [ scc.merge] INFO - PR 71 sbesson 'Bump Bio-Formats to version 7.1.0' 2024-03-14 15:41:44,490 [ scc.merge] INFO - PR 74 dgault 'JZarr: Add jackson.core and jackson-databind to exclsions' 2024-03-14 15:41:44,490 [ scc.merge] INFO - PR 75 dgault 'Update handling and parsing of acquisition metadata' 2024-03-14 15:41:44,490 [ scc.merge] INFO - PR 80 jburel 'Review action' 2024-03-14 15:41:44,490 [ scc.merge] INFO - PR 81 jburel 'add Java 17 to testing matrix' 2024-03-14 15:41:44,490 [ scc.merge] INFO - PR 82 dgault 'Reintroduce S3FileSystemStore' 2024-03-14 15:41:44,490 [ scc.merge] INFO 2024-03-14 15:41:44,490 [ scc.merge] INFO Repository: ome/bio-formats-documentation 2024-03-14 15:41:44,491 [ scc.merge] INFO Already up to date. 2024-03-14 15:41:44,491 [ scc.merge] INFO 2024-03-14 15:41:44,491 [ scc.merge] INFO 2024-03-14 15:41:44,491 [ scc.merge] INFO Repository: ome/bio-formats-examples 2024-03-14 15:41:44,491 [ scc.merge] INFO Already up to date. 2024-03-14 15:41:44,491 [ scc.merge] INFO 2024-03-14 15:41:44,491 [ scc.merge] INFO Merged PRs: 2024-03-14 15:41:44,491 [ scc.merge] INFO - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop' 2024-03-14 15:41:44,491 [ scc.merge] INFO 2024-03-14 15:41:44,491 [ scc.merge] INFO Repository: openmicroscopy/bioformats 2024-03-14 15:41:44,491 [ scc.merge] INFO Excluded PRs: 2024-03-14 15:41:44,491 [ scc.merge] INFO - PR 4164 melissalinkert 'Reduce DICOM write time' (stage: draft) 2024-03-14 15:41:44,491 [ scc.merge] INFO - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure) 2024-03-14 15:41:44,491 [ scc.merge] INFO - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) 2024-03-14 15:41:44,491 [ scc.merge] INFO - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) 2024-03-14 15:41:44,491 [ scc.merge] INFO - PR 3898 melissalinkert 'InCell 1000/2000 field count and plane metadata fixes' (stage: draft) 2024-03-14 15:41:44,491 [ scc.merge] INFO - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) 2024-03-14 15:41:44,491 [ scc.merge] INFO - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15) 2024-03-14 15:41:44,491 [ scc.merge] INFO - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) 2024-03-14 15:41:44,491 [ scc.merge] INFO - PR 3537 dgault 'Flex: Merge IDR changes and add new group plate option' (label: exclude) 2024-03-14 15:41:44,491 [ scc.merge] INFO Already up to date. 2024-03-14 15:41:44,491 [ scc.merge] INFO 2024-03-14 15:41:44,491 [ scc.merge] INFO Merged PRs: 2024-03-14 15:41:44,491 [ scc.merge] INFO - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1' 2024-03-14 15:41:44,491 [ scc.merge] INFO - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' 2024-03-14 15:41:44,491 [ scc.merge] INFO - PR 4147 TBlackmore 'Added support for ColumbusReader to import data with z stacks' 2024-03-14 15:41:44,491 [ scc.merge] INFO - PR 4154 melissalinkert 'Update GitHub actions versions and add M1/Java 21 build' 2024-03-14 15:41:44,491 [ scc.merge] INFO - PR 4159 melissalinkert 'Turn off file-leak-detector if tests are run with Java 21' 2024-03-14 15:41:44,491 [ scc.merge] INFO - PR 4162 melissalinkert 'Remove duplicate enum check and add clarifying comment' 2024-03-14 15:41:44,491 [ scc.merge] INFO - PR 4163 melissalinkert 'SimplePCI: fix Z position handling' 2024-03-14 15:41:44,491 [ scc.merge] INFO 2024-03-14 15:41:44,491 [ scc.merge] INFO Repository: ome/ome-codecs 2024-03-14 15:41:44,491 [ scc.merge] INFO Excluded PRs: 2024-03-14 15:41:44,491 [ scc.merge] INFO - PR 24 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (status: failure) 2024-03-14 15:41:44,491 [ scc.merge] INFO - PR 21 dgault 'Replace one-jai with jai-imageio-jpeg2000' (stage: draft) 2024-03-14 15:41:44,491 [ scc.merge] INFO Already up to date. 2024-03-14 15:41:44,491 [ scc.merge] INFO 2024-03-14 15:41:44,491 [ scc.merge] INFO Merged PRs: 2024-03-14 15:41:44,491 [ scc.merge] INFO - PR 36 sbesson 'Use Maven profiles to handle different versions of TestNG' 2024-03-14 15:41:44,491 [ scc.merge] INFO 2024-03-14 15:41:44,491 [ scc.merge] INFO Repository: ome/ome-common-java 2024-03-14 15:41:44,491 [ scc.merge] INFO Excluded PRs: 2024-03-14 15:41:44,492 [ scc.merge] INFO - PR 72 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (label: exclude) 2024-03-14 15:41:44,492 [ scc.merge] INFO - PR 59 NicoKiaru 'adds AverageImageScaler implementation of IImageScaler' (user: NicoKiaru) 2024-03-14 15:41:44,492 [ scc.merge] INFO Already up to date. 2024-03-14 15:41:44,492 [ scc.merge] INFO 2024-03-14 15:41:44,492 [ scc.merge] INFO Merged PRs: 2024-03-14 15:41:44,492 [ scc.merge] INFO - PR 88 sbesson 'Use Maven profiles to handle different versions of TestNG' 2024-03-14 15:41:44,492 [ scc.merge] INFO 2024-03-14 15:41:44,492 [ scc.merge] INFO Repository: ome/ome-jai 2024-03-14 15:41:44,492 [ scc.merge] INFO Already up to date. 2024-03-14 15:41:44,492 [ scc.merge] INFO 2024-03-14 15:41:44,492 [ scc.merge] INFO Merged PRs: 2024-03-14 15:41:44,492 [ scc.merge] INFO - PR 7 melissalinkert 'Add JDK21 to build matrix' 2024-03-14 15:41:44,492 [ scc.merge] INFO 2024-03-14 15:41:44,492 [ scc.merge] INFO Repository: ome/ome-mdbtools 2024-03-14 15:41:44,492 [ scc.merge] INFO Already up to date. 2024-03-14 15:41:44,492 [ scc.merge] INFO 2024-03-14 15:41:44,492 [ scc.merge] INFO Merged PRs: 2024-03-14 15:41:44,492 [ scc.merge] INFO - PR 13 melissalinkert 'Add JDK 21 to build matrix' 2024-03-14 15:41:44,492 [ scc.merge] INFO 2024-03-14 15:41:44,492 [ scc.merge] INFO Repository: ome/ome-metakit 2024-03-14 15:41:44,492 [ scc.merge] INFO Updating 8ead2f6..21bd756 2024-03-14 15:41:44,492 [ scc.merge] INFO Previously merged: 2024-03-14 15:41:44,492 [ scc.merge] INFO - PR 20 melissalinkert 'Add JDK 21 to build matrix' 2024-03-14 15:41:44,492 [ scc.merge] INFO 2024-03-14 15:41:44,492 [ scc.merge] INFO Merged PRs: 2024-03-14 15:41:44,492 [ scc.merge] INFO - PR 21 sbesson 'Use Maven profiles to handle different versions of TestNG' 2024-03-14 15:41:44,492 [ scc.merge] INFO 2024-03-14 15:41:44,492 [ scc.merge] INFO Repository: ome/ome-model 2024-03-14 15:41:44,492 [ scc.merge] INFO Excluded PRs: 2024-03-14 15:41:44,492 [ scc.merge] INFO - PR 180 joshmoore 'xsd-fu: templates for linkml generation' (stage: draft) 2024-03-14 15:41:44,492 [ scc.merge] INFO Already up to date. 2024-03-14 15:41:44,492 [ scc.merge] INFO 2024-03-14 15:41:44,492 [ scc.merge] INFO Merged PRs: 2024-03-14 15:41:44,492 [ scc.merge] INFO - PR 185 melissalinkert 'Add model object API to clear each list of associated objects' 2024-03-14 15:41:44,492 [ scc.merge] INFO - PR 187 melissalinkert 'Add JDK 21 to build matrix' 2024-03-14 15:41:44,492 [ scc.merge] INFO - PR 188 sbesson 'Use Maven profiles to handle different versions of TestNG' 2024-03-14 15:41:44,492 [ scc.merge] INFO 2024-03-14 15:41:44,492 [ scc.merge] INFO Conflicting PRs (not included): 2024-03-14 15:41:44,492 [ scc.merge] INFO - PR 174 jburel 'Remove docs' 2024-03-14 15:41:44,492 [ scc.merge] INFO 2024-03-14 15:41:44,492 [ scc.merge] INFO Repository: ome/ome-poi 2024-03-14 15:41:44,493 [ scc.merge] INFO Already up to date. 2024-03-14 15:41:44,493 [ scc.merge] INFO 2024-03-14 15:41:44,493 [ scc.merge] INFO Merged PRs: 2024-03-14 15:41:44,493 [ scc.merge] INFO - PR 15 sbesson 'Add JDK 21 to the build matrix' 2024-03-14 15:41:44,493 [ scc.merge] INFO 2024-03-14 15:41:44,493 [ scc.merge] INFO Repository: ome/ome-stubs 2024-03-14 15:41:44,493 [ scc.merge] INFO Already up to date. 2024-03-14 15:41:44,493 [ scc.merge] INFO 2024-03-14 15:41:44,493 [ scc.merge] INFO Merged PRs: 2024-03-14 15:41:44,493 [ scc.merge] INFO - PR 11 melissalinkert 'Add JDK 21 to build matrix' 2024-03-14 15:41:44,493 [ scc.merge] INFO 2024-03-14 15:42:09,828 [ scc.merge] INFO Merged branch pushed to https://github.com/snoopycrimecop/bio-formats-build/tree/merge_ci + echo 'Update maven component versions' Update maven component versions + update-versions OMEZarrReader=0.4.2-SNAPSHOT bio-formats-documentation=8.0.0-SNAPSHOT bio-formats-examples=8.0.0-SNAPSHOT bio-formats_plugins=8.0.0-SNAPSHOT bio-formats-tools=8.0.0-SNAPSHOT bioformats_package=8.0.0-SNAPSHOT turbojpeg=8.0.0-SNAPSHOT formats-api=8.0.0-SNAPSHOT formats-bsd=8.0.0-SNAPSHOT formats-gpl=8.0.0-SNAPSHOT test-suite=8.0.0-SNAPSHOT pom-bio-formats=8.0.0-SNAPSHOT bioformats=8.0.0-SNAPSHOT ome-codecs=1.0.2-SNAPSHOT ome-common=6.0.22-SNAPSHOT ome-jai=0.1.3-SNAPSHOT ome-mdbtools=5.3.3-SNAPSHOT metakit=5.3.7-SNAPSHOT ome-model-doc=6.3.5-SNAPSHOT ome-xml=6.3.5-SNAPSHOT specification=6.3.5-SNAPSHOT ome-model=6.3.5-SNAPSHOT ome-poi=5.3.9-SNAPSHOT mipav-stubs=6.0.2-SNAPSHOT ome-stubs=6.0.2-SNAPSHOT + echo 'Commit all component version changes' Commit all component version changes + git submodule foreach 'git add -u' Entering 'ZarrReader' Entering 'bio-formats-documentation' Entering 'bio-formats-examples' Entering 'bioformats' Entering 'ome-codecs' Entering 'ome-common-java' Entering 'ome-jai' Entering 'ome-mdbtools' Entering 'ome-metakit' Entering 'ome-model' Entering 'ome-poi' Entering 'ome-stubs' + git submodule foreach 'git commit -m '\''Update component versions'\'' || true' Entering 'ZarrReader' HEAD detached from cf4f3f2 nothing to commit, working tree clean Entering 'bio-formats-documentation' [detached HEAD 5d06aaaf] Update component versions 1 file changed, 7 insertions(+), 7 deletions(-) Entering 'bio-formats-examples' [detached HEAD 7881d68] Update component versions 1 file changed, 1 insertion(+), 1 deletion(-) Entering 'bioformats' [detached HEAD f94707a843] Update component versions 1 file changed, 9 insertions(+), 9 deletions(-) Entering 'ome-codecs' [detached HEAD 63b8d4b] Update component versions 1 file changed, 2 insertions(+), 2 deletions(-) Entering 'ome-common-java' HEAD detached from eca9c1c nothing to commit, working tree clean Entering 'ome-jai' HEAD detached from 6b7e421 nothing to commit, working tree clean Entering 'ome-mdbtools' HEAD detached from cdb3552 nothing to commit, working tree clean Entering 'ome-metakit' [detached HEAD 2338588] Update component versions 1 file changed, 1 insertion(+), 1 deletion(-) Entering 'ome-model' [detached HEAD a45ab065] Update component versions 1 file changed, 1 insertion(+), 1 deletion(-) Entering 'ome-poi' [detached HEAD 7f9542d] Update component versions 1 file changed, 1 insertion(+), 1 deletion(-) Entering 'ome-stubs' HEAD detached from a17529e nothing to commit, working tree clean + echo 'Push all branches' Push all branches ++ git config github.user + user=snoopycrimecop + git submodule foreach 'git push -f git@github.com:snoopycrimecop/${path}.git HEAD:merge_ci' Entering 'ZarrReader' Everything up-to-date Entering 'bio-formats-documentation' To github.com:snoopycrimecop/bio-formats-documentation.git 661f1bcd..5d06aaaf HEAD -> merge_ci Entering 'bio-formats-examples' To github.com:snoopycrimecop/bio-formats-examples.git e9ad5ed..7881d68 HEAD -> merge_ci Entering 'bioformats' To github.com:snoopycrimecop/bioformats.git 1ebed53d77..f94707a843 HEAD -> merge_ci Entering 'ome-codecs' To github.com:snoopycrimecop/ome-codecs.git dbce919..63b8d4b HEAD -> merge_ci Entering 'ome-common-java' Everything up-to-date Entering 'ome-jai' Everything up-to-date Entering 'ome-mdbtools' Everything up-to-date Entering 'ome-metakit' To github.com:snoopycrimecop/ome-metakit.git 8ee2483..2338588 HEAD -> merge_ci Entering 'ome-model' To github.com:snoopycrimecop/ome-model.git 6919ee42..a45ab065 HEAD -> merge_ci Entering 'ome-poi' To github.com:snoopycrimecop/ome-poi.git e17eedb..7f9542d HEAD -> merge_ci Entering 'ome-stubs' Everything up-to-date + echo 'Commit all component version changes' Commit all component version changes + git add -u + git commit -m 'Update component versions' [detached HEAD 1612f4f] Update component versions 7 files changed, 7 insertions(+), 7 deletions(-) + git push -f git@github.com:snoopycrimecop/bio-formats-build.git HEAD:merge_ci To github.com:snoopycrimecop/bio-formats-build.git e24fcb2..1612f4f HEAD -> merge_ci [BIOFORMATS-push] $ /bin/bash -xe /tmp/jenkins9770641833888561744.sh + mkdir -p /home/omero/workspace/BIOFORMATS-push/target + cd /home/omero/workspace/BIOFORMATS-push/target + curl -sfL https://github.com/ome/build-infra/archive/master.tar.gz + tar -zxf - + export PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/omero/workspace/BIOFORMATS-push/target/build-infra-master/ + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/omero/workspace/BIOFORMATS-push/target/build-infra-master/ + cd /home/omero/workspace/BIOFORMATS-push/bio-formats-build + foreach-get-version + foreach-get-version-as-property Archiving artifacts Finished: SUCCESS